COMPASS

This is an example of COMPASS output produced by running this query against PDB database 
COMPASS 3.0
Reference:
Ruslan I. Sadreyev and Nick V. Grishin (2003) COMPASS: a tool for comparison
of multiple protein alignments with assessment of statistical significance.
J Mol. Biol. 326(1):317-36
Job ID: JOB_unRIK0

Query = QUERY  Input processed by alignment reader (please check!)
length=173; filtered_length=173; Neff=3.017
(threshold of effective gap content in columns: 0.5)

Database: PDB70_iter5
Effective database length used: 3663686


COMPASS alignment format:
CAPITAL letters: residues at positions aligned by COMPASS (input alignment positions with gap content < 0.5)
lower-case letters: residues at positions not used by COMPASS (input alignment positions with gap content >= 0.5)
'-' : gaps retained from original alignments at positions aligned by COMPASS (positions with gap content < 0.5)
'.' : gaps retained from original alignments at positions not used by COMPASS (positions with gap content >= 0.5)
'=' : gaps introduced by COMPASS in profile-profile alignment
'~' : gaps introduced by COMPASS against positions that are not used in the construction of profile-profile alignment
      (positions with gap content >= 0.5)

Clickable sequence names: links to full alignments.
For more details, see documentation.


                Hits with E-value BETTER than threshold:

Profiles producing significant alignments:                    Score   E-value
2F6SA   Structure Of Cell Filamentation Protein (Fic) From He  391        0.00e+00
2G03A   Structure Of A Putative Cell Filamentation Protein Fr  405        0.00e+00
3CUCA   Crystal Structure Of Protein Of Unknown Function With  122        7.15e-10



 Hits with E-value WORSE than threshold (may be not biologically meaningful):

2A0ZA   The Molecular Structure Of Toll-Like Receptor 3 Ligan  72        9.39e-02
2QC0A   Crystal Structure Of Uncharacterized Protein (Np_7197  69        1.89e-01



                             Alignments:







Subject = 2F6SA   Structure Of Cell Filamentation Protein (Fic) From He


 Structure   Next 10











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Query




 



Subjct


 









length=180  filtered_length=160  Neff=14.512
Smith-Waterman score = 391   Evalue = 0.00e+00

2F6S-A        2      RQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANC  61
CONSENSUS_1   2      RLSKKKAKELFDSGLLDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVNIAKGNFRFAPL  61
                     +L++K+A+EL++SGLLD+LE+GT+KGL++IH++LFGD+YD+AGK+R+VNI+KG+FRFAP+
CONSENSUS_2   7      ILELKNALELIESGLLDELEPGTLKGLKEIHRLLFGDIYDWAGKFRTVNISKGGFRFAPP  66
2F6SA         7      RQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANC  66

2F6S-A        62     LYLDLILPRIESXPQNNFNQIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKELKKIVLW  121
CONSENSUS_1   62     LFLDLALKKIDKLPENTFDEIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKELKKVVDW  121
                     +++++ L++++KL+++TF+E++E+++E+N++HPFR+GNGR++R++L+LLLKK+++K++DW
CONSENSUS_2   67     EYIEPLLDELEKLKQETFEELAEFHAELNVIHPFRDGNGRTGRLLLNLLLKKAGGKPIDW  126
2F6SA         67     LYLDLILPRIESMPQNNFNQIVEKYVEMNIAHPFLEGNGRATRIWLDLLLKKELKKIVLW  126

2F6S-A        122    DRIDKAAYLSAXERSPVNDLEIKTLLKKHL~SSNTNDPLTLI  162
CONSENSUS_1   122    SRIDKDDYLLAMERSPVDDLELKHLLKKAL~TDKINDREVFL  162
                     S++DK++YL+A+ERSPV+DLELK+LLKKA  TD+IN+REVF+
CONSENSUS_2   127    SKVDKEEYLEALERSPVKDLELKFLLKKA=.TDLINNREVFI  167
2F6SA         127    DRIDKAAYLSAMERSPVNDLEIKTLLKKH=lSSNTNDPLTLI  167








Subject = 2G03A   Structure Of A Putative Cell Filamentation Protein Fr


 Structure











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Downloads:       
PDB file   
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Database links:   
PDB
   
SCOP
   
CATH
   
NCBI








Query



 



Subjct


 









length=177  filtered_length=162  Neff=14.531
Smith-Waterman score = 405   Evalue = 0.00e+00

2F6S-A        2      RQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANC  61
CONSENSUS_1   2      RLSKKKAKELFDSGLLDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVNIAKGNFRFAPL  61
                     +L++++AK+LF+SGLLD+LE+GT+KGL++IH++LFGDLYD+AGK+R+VNI+KG+F+FAP 
CONSENSUS_2   6      ELELENAKALFESGLLDELEPGTLKGLKEIHRLLFGDLYDWAGKFRTVNISKGGFVFAPP  65
2G03A         6      EQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANA  65

2F6S-A        62     LYLDLILPRIESXPQNNFNQIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKELKKIVLW  121
CONSENSUS_1   62     LFLDLALKKIDKLPENTFDEIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKELKKVVDW  121
                     ++L++ L++++KL+E++F+E++E+++E+N++HPFR+GNGR++R++LDL+L+KE+++++DW
CONSENSUS_2   66     EYLEDLLEELEKLDEELFEELAEFHAELNVIHPFRDGNGRTGRLLLDLILAKEAGYPLDW  125
2G03A         66     MYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNW  125

2F6S-A        122    DRIDKAAYLSAXERSPVNDLEIKTLLKKHLSSNTNDPLTLIK  163
CONSENSUS_1   122    SRIDKDDYLLAMERSPVDDLELKHLLKKALTDKINDREVFLK  163
                     SRIDK++YL+A++RSPV+DLELK+LLKKALTDKINDREVFLK
CONSENSUS_2   126    SRIDKEEYLEALIRSPVGDLELKELLKKALTDKINDREVFLK  167
2G03A         126    QNVSKTLYLQAMERSPVNDLELRFLLKDNLTDDVDNREIIFK  167








Subject = 3CUCA   Crystal Structure Of Protein Of Unknown Function With


 Structure











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Downloads:       
PDB file   
PyMOL


Database links:   
PDB
   
SCOP
   
CATH
   
NCBI








Query




 



Subjct


 









length=262  filtered_length=254  Neff=18.039
Smith-Waterman score = 122   Evalue = 7.15e-10

2F6S-A        3      QSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKN===IAKGNFRFA  59
CONSENSUS_1   3      LSKKKAKELFDSGLLDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVN===IAKGNFRFA  59
                     L  K+A EL ++ L +  E  T + + ++H+ L+++L+++AG++R+ +   I++G F+++
CONSENSUS_2   71     LNHKEALELILELLKSKEEPLTEDLILELHRLLLRGLLEDAGEFRRRDNVIIGGGVFVPP  130
3CUCA         71     KAHNVGLEMIKQEAQDKERPLTESFIRELNRTILVQDYWKVGEYKSRPNSVLTGEVFSYA  130

2F6S-A        60     NCLYLDLILPRIESXPQNNFNQIVEKYVEXNI========AHPFLEGNGRATRIWLDLLL  111
CONSENSUS_1   60     PLLFLDLALKKIDKLPENTFDEIIEKYVEMNI========AHPFREGNGRATRIWLDLLL  111
                     P   +++ L+++ ++ +++ D+ +   +++ +        +HPF++GNGR +R++L+LLL
CONSENSUS_2   131    PPEEVPALLEELLDWLNSEEDKGDLDPLIRAALLHFRFVYIHPFLDGNGRTGRLLLNLLL  190
3CUCA         131    SPEETPAFMTSLVDWYNLEADKGILTPVELAALLHYRYIRIHPFEDGNGRIARLLVNFVL  190

2F6S-A        112    KKELKKIVLWDRIDKAAYLSAXERSPVNDLEIKTLLKKHLSSNTNDPLTLI=KGITQSY  169
CONSENSUS_1   112    KKELKKVVDWSRIDKDDYLLAMERSPVDDLELKHLLKKALTDKINDREVFL=KGIDASY  169
                      ++   ++ + + D+D+Y++A+E++ V  L  ++   ++ ++++ +   F+ +++++S+
CONSENSUS_2   191    LRAGYPLSIIIKEDRDEYYDALEAADVGGLGDLDGRWNLNEGDLTPFIEFFLEALEESL  249
3CUCA         191    HRYGYPMIVIHSEDKSNYLNILHQCDVEAGLTPSDGANATLNDILPFVNYLSSCLIRSL  249








Subject = 2A0ZA   The Molecular Structure Of Toll-Like Receptor 3 Ligan


 Structure




length=671  filtered_length=668  Neff=20.855
Smith-Waterman score = 72   Evalue = 9.39e-02

2F6S-A        17     IDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFAN===========CLYLD  65
CONSENSUS_1   17     LDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVNIAKGNFRFAP===========LLFLD  65
                     L +L +   K L++++  L+G+L     ++R ++++ +++++ +            L+L+
CONSENSUS_2   539    LKVLDLSGNK=LSGLPPGLLGGLT====SLRVLDLSGNRLSGLIPGLLGNLTSLEVLDLS  593
2A0ZA         539    LHILNLESNG=FDEIPVEVFKDLF====ELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQ  593

2F6S-A        66     LILPRIESXPQNNFNQIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKELKKIVLWDRID  125
CONSENSUS_1   66     LALKKIDKLPENTFDEIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKELKKVVDWSRID  125
                      +  K+  L+++++ +++ +   +++ +   +++ ++++  LD+L +++++++ + +++ 
CONSENSUS_2   594    NN==KLSGLIPSLLGDLLSSLSVLDLSGNPLLCDCDNLGWFLDWLNESNVTLPGLADDV=  650
2A0ZA         594    KN==LITSVEKKVFGPAFRNLTELDMRFNPFDCTCESIAWFVNWINETHTNIPELSSHY=  650

2F6S-A        126    KAAYLSAXERSPVNDLEI  143
CONSENSUS_1   126    KDDYLLAMERSPVDDLEL  143
                     + ++++++++ P+ DL+L
CONSENSUS_2   651    LCASPPSLRGKPLLDLDL  668
2A0ZA         651    LCNTPPHYHGFPVRLFDT  668








Subject = 2QC0A   Crystal Structure Of Uncharacterized Protein (Np_7197


 Structure




length=367  filtered_length=353  Neff=16.986
Smith-Waterman score = 69   Evalue = 1.89e-01

2F6S-A        28     LQEIHRFLFEGLYEF===AGKIRDKNIAKGNFRFANCLY==LDLILPRIESXPQNNFN==  80
CONSENSUS_1   28     LADIHKYLFGDLYDF===AGKIRDVNIAKGNFRFAPLLF==LDLALKKIDKLPENTFD==  80
                     + ++H+ L++++ ++    G++R+ ++  G + F P  +  L++ L+++++  +++ D  
CONSENSUS_2   122    ILELHRLLLSGGRGERKVPGEFRRSQNTGGIVHFPPPPPELLPELLDDLEDFLNDEDDLD  181
2QC0A         122    ALEICSTIKSVQMDVRKVPGTSLTNQATGEVIYTPPAGESVIRDLLSNWEAFLHNQDDVD  181

2F6S-A        81     ===QIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKE  114
CONSENSUS_1   81     ===EIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKE  114
                        +++  ++++   HPF++GNGR +R++++LLL ++
CONSENSUS_2   182    PLIRAALAHFQFETIHPFLDGNGRIGRLLITLLLARK  218
2QC0A         182    PLIKMAMAHYQFEAIHPFIDGNGRTGRVLNILYLIDQ  218













Parameters:
E-value cutoff: 1.000e+00
Maximal number of hits to display: 100
Lambda_ungapped: 3.1760e-01
Expected value of positional scores: -5.2090e-01
Gap opening: 10
Gap extension: 1