[modeller_usage] regarding N terminus region

["simran jeet" <>]

I have a protein sequence whose N terminus region does not matches with the template. Is it neccessary that N and C terminus regions of a protein should be fixed for homology modeling? The n terminus region contains 12 residues.  There are long gaps also within the alignment. Can these regions be modelled by loop modelling? I am also attaching the alignment file. 
>P1;1o98A
structureX:1o98.pdb:   2 :A:+509 :A:undefined:undefined:-1.00:-1.00
------------SKKPVALIILDGFALRDETYGNAVAQANKPNFDRYWNE-YPHTTLKACGEAVGLPE-GQMGNS
EVGHLNIGAGRIVYQSLTRINIAIREGEFDRNETFLAAMNHVKQHGTSLHLFGLLSDGGVHSHIHHLYALLRLAA
KEGVKRVYIHGFLDGRDVGPQTAPQYIKELQEKIKEYGVGEIATLSGRYYSMDRDK------RWDRVEKAYRAMV
YGEGPTYRDPLECIEDSYKHG--IYDEFVLPSVIVREDGRPVATIQDNDAIIFYNFRPDRAIQISNTFTNEDFRE
FDRGPKHPKHLFFVCLTHFSETVAGYVAFKPTNLDNTIGEVLSQHGLRQLRIAETEKYPHVTFFMSGGREEEFP-
GEDRILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNYANPDMVGHSGKLEPTIKAVEAVDECLGKV
VDAILAKGGIAIITADHGNADEVLTPDGK------------PQTAHTTNPVPVIVTKKGIKLRD-------GGIL
GDLAPTMLDLLGLPQPKEMTGKSLIV---*

>P1;IPGM
sequence:IPGM:     : :     : :::-1.00:-1.00
MSALSLQLHTALPRRKLLLVVMDGVGIGPGDEYDAVHVAKTPFIDSMCADAKHFRSVCAHGTAVGLPTDADMGNS
EVGHNALGSGRVVLQGASLVDDAIKTGEIFTSDGYRYLHGAFSQPGRTLHLIGLLSDGGVHSRDNQLYEIINHAS
SNGAKRIRLHVLYDGRDVPDKSSFKFTDDLESVLEKARAKGCDARIASGGGRMFVTMDRYEADWSVVERGWRAQV
LGEARAFASAGEAIKTFRKEDPNVSDQYYPPFIISDVDGKAIGPIEDGDAVLCFNFRGDRVIEMSRAFEEEDFDK
FNRVRVPKVRYAGMMRYDGDLGIPNNFLVPPPRLSRTSEEYLVGSGCNIFACSETQKFGHVTYFWNGNRSGKLDE
EHETFFEIPSDRVQFNEKPLMKSKEITEAAIEALKSGKYDVVRINFPNGDMVGHTGDLAATVTAVEAVDASLQRL
KEAVDAVNGVFLITADHGNSDDMAQRDKKGKPILGKDGKVLPLTSHTLAPVPVFIGGAGLDARVQMRTGLPKAGL
ANVTATFLNLMGFTAPTDYEPSLIEVIPN*