# A sample TOP file for fully automated comparative modeling INCLUDE # include MODELLER routines SET ATOM_FILES_DIRECTORY = './:../HYPO' # directory with input atom files SET ALNFILE = 'alignment.ali' # input file w/ templates and target SET KNOWNS = '2PIA' '1GVH' '1TVC' '1KRH' '2CND' '1QGA' '1H42' '1FNC' '1RFK' # templates' PDB codes SET SEQUENCE = 'reduct' # target code SET STARTING_MODEL = 1 SET ENDING_MODEL = 3 SET HETATM_IO = ON SET OUTPUT_CONTROL = 1 1 1 1 1 CALL ROUTINE = 'model' # get alignment and a model
>P1;2PIA
StructureX:2PIA :8: :320: :Oxido:HUM: :
FLRLKIASKEKIARD--IWSFELTDPQGAPLPPFEAGANLTVAVPNGS---RRTYSLCNDS
QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVSLPRNEF---PLDKRAKSFILVAGGI
GITPMLSMARQ-LR--AEGLRSFRLYYLTRDPEGTAFFDELTS--DEW-------------
-------------------------------------------------------------
------------------NTNARENTPFTVRLSRSGTSFEIPANRS--ILEVLRDANVRVP
SSCESGTCGSCKTALCSGEADH-RDMVLRDDE--KGTQIMVCVSRAKSAELVLD*
>P1;1GVH
StructureX:1GVH :212: A :261:A :oxido:uk2: :
------------------------------------------------------------P
D-GKGYRIAVKREEGGQVSNWLH-NHANVGDVVKLVAPAGDFFMAVADDTP----------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
------------------------------------------------------*
>P1;1TVC
StructureX:1TVC :44:A:248:A :oxidored:uk3: :
---------------------------------FEPGQFMDLT--IPGTDVSRSYSPANLP
NPEGRLEFLIRVLPEGRFSDYLRNDARVGQVLSVKGPL-----------------------
-------------------------------------------------------------
----------------------------------LCGPPGMID-AACELVRSRGIPGEQVF
FEKF---LPSG--------------------------------------------------
------------------------------------------------------*
>P1;1KRH
StructureX:1KRH :295:B: 327:B :Oxidored:uk4: :
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL
FEKFSAN------------------------------------------------------
------------------------------------------------------*
>P1;2CND
StructureX:2CND :145: :257: :oxidored:uk5: :
-------------------------------------------------------------
-----------------------------------------------------------GS
GITPMYQIIQAVLRDQPEDHTEMHLVYANRTEDDILLRDELDRWAAEYPDRLKVWYVIDQV
KRPEEGWKYSVGFV-TEAVLREHVPEGGDDTLALACGPPPMIQFAISPNLE----------
-------------------------------------------------------------
------------------------------------------------------*
>P1;1QGA
StructureX:1QGA :194:B :231:B :oxidored:uk6: :
-------------------------------------------------------------
-------------------------------------------------------------
------------------------LFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSRE
Q------------------------------------------------------------
-------------------------------------------------------------
------------------------------------------------------*
>P1;1H42
StructureX:1H42 :190:A :235:A :ZNFING:HUM: :
-------------------------------------------------------------
-------------------------------------------------------------
------------------------LVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISRE
QKNPQ--GGR---------------------------------------------------
-------------------------------------------------------------
------------------------------------------------------*
>P1;1FNC
StructureX:1FNC :234: :281: :ZNFING:HUM: :
-------------------------------------------------------------
-------------------------------------------------------------
----------------------------------------------------------SRE
QTNEKGEKMYIQTRMAQYAVELWEMLKKDNTYVYMCGLKG-MEKGI---------------
-------------------------------------------------------------
------------------------------------------------------*
>P1;1RFK
StructureX:1RFK :4: B :91:B :ZNFING:HUM: :
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------------------KVTLINEAEGLNKTIEVPDDQYILDAAEEAGIDLP
YSCRAGACSTCAGKLISGTVDQSDQSFLDDDQIEAGYVLT-CVAYPTSDCVIET*
>P1;reduct
Sequence:reduct:1 : :344 : :hypo:unknown: :
FHDMRVASVRPETRDAIVVTFDVP-PSLADSFHYAPGQHLTLRTEIGGEDVRRSYSICSGA
D-ERALRIAIKRVHGGLFSNWAN-DFMKPGVSVEVMPPSGHFGVAPDPQHHRNYAAFAAGS
GITPILSQIKTILA--AEQGSRFTLVYGNRSSSSVMFREELADLKDQYGERLNLVHVLSRE
QQDIELFNGRIDRERCDALLTRWIDAKRID-VAFICGPMDMME-AVSASLQAHGVAKSAIK
MELFATSLPKGPRPVHSHPVKGTEDCEVTVIQDGRVRQFTMPKNRDS-VLDAGLGQGIEMP
YSCKGGVCSTCRCKVIDGEVDHDTNFALEDYEIARGFRLS-CQSYPVTDKLVLD*
Attachment:
q96c401.log
Description: 2796389291-q96c401.log