Alignments for a candidate for trpE in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Methanosarcina acetivorans C2A

Align Anthranilate synthase component 1 2; EC 4.1.3.27; Anthranilate synthase component I 2 (uncharacterized)
to candidate WP_011022927.1 MA_RS15665 anthranilate synthase component I

Query= curated2:Q5V213
         (536 letters)



>NCBI__GCF_000007345.1:WP_011022927.1
          Length = 560

 Score =  404 bits (1037), Expect = e-117
 Identities = 248/576 (43%), Positives = 328/576 (56%), Gaps = 87/576 (15%)

Query: 1   MTLDISREEFVEHAKA-DRPVVVRTAAELD---VDVEPLTAYAALTGRTSDVAANDYTFL 56
           ++ D+ +EEF+E     ++P +V+  A+++       PL  Y AL G         Y++L
Sbjct: 2   LSFDLGKEEFLELVSGLEKPGLVQLFAKVEGCSPACSPLELYGALRGS----GTTGYSYL 57

Query: 57  LESAEKVASSDPDGAFAPETDDRHARFSFVGYDPRAVVTVTGDESEVEAFDDRYADLVTT 116
           LES EK  S               AR+SFVG DP AV+ +   +  +E  + + + L   
Sbjct: 58  LESVEKQES--------------RARYSFVGNDPDAVLKINDRKISLELLNPKASPLFEA 103

Query: 117 ----------------------------------DGGDVVDDLRAAMPD---VALRNFPA 139
                                              G DV D LR A P    + L N   
Sbjct: 104 ICTKMEEVCGPETAEKENESKKNAGPEKFTAAIPRGKDVFDALRLAFPPANGIELLNSRR 163

Query: 140 MDRQHLEGGLVGFLSYDAVYDLWLDEVGLDRP-DSRFPDAQFVLTTSTVRFDHVEDTVSL 198
             RQ   GG +G+ +YDA+YD WL   G+++  +S  PD Q++L + +   DH+ + V +
Sbjct: 164 FARQTFLGGAIGYTAYDAIYDSWL---GVEKGFESDIPDLQYLLVSKSFVLDHLTEEVYI 220

Query: 199 VFTPVVRQGEDAGERYGELVAEAERVEAVLS------DLSPLSTGGFRREDEVAGP---- 248
           V TP V  G DA + Y E ++EAER  +V+       D +  + G      +V+GP    
Sbjct: 221 VLTPFVSPGSDAEQVYEEALSEAERFYSVIKKATQPEDAAKAAEGIIASGTDVSGPAKAP 280

Query: 249 ----------RDEYEDAVERAKEYVLSGDIYQGVISRTRELYGDVDPLGFYEALRAVNPS 298
                     R  +E++V +AKE++ +GDI+Q V+SR  E   +  P   Y  LRA+NPS
Sbjct: 281 NSNVQVCSVDRSGFEESVLQAKEHIFAGDIFQVVLSRKCEFKMEQSPFELYIQLRAINPS 340

Query: 299 PYMYLLGYDDLTIVGASPETLVSVAGDHVVSNPIAGTCPRGNSPVEDRRLAGEMLADGKE 358
           PYMY+  + DL IVGASPETL++V    V+ NPIAGTCPRG S  ED  LA  ML D KE
Sbjct: 341 PYMYIFEFGDLAIVGASPETLLTVHKRTVIINPIAGTCPRGKSEAEDETLASHMLNDEKE 400

Query: 359 RAEHTMLVDLARNDVRRVAEAGSVRVPEFMNVLKYSHVQHIESTVTGRLAEDKDAFDAAR 418
           RAEH MLVDL RNDVR V+E+GSV+V  FM VLKYSHVQHIESTV+G L  + D FDA R
Sbjct: 401 RAEHVMLVDLGRNDVRMVSESGSVKVSGFMKVLKYSHVQHIESTVSGTLRPECDQFDAFR 460

Query: 419 ATFPAGTLSGAPKIRAMEIIDELERSPRGPYGGGVGYFDWDGDTDFAIVIRSATVEDEGD 478
           A FPAGTLSGAPKIRAMEII E E  PRG YGGGVGY+ W+GD DFAIVIR+  ++    
Sbjct: 461 AVFPAGTLSGAPKIRAMEIISEREAVPRGIYGGGVGYYSWNGDADFAIVIRTLLIQGR-- 518

Query: 479 RDRITVQAGAGIVADSDPESEYVETEQKMDGVLTAL 514
             + +VQAGAGIVADSDP  E+ ET++KM  +LTA+
Sbjct: 519 --KASVQAGAGIVADSDPAYEFRETDRKMAAMLTAI 552


Lambda     K      H
   0.315    0.135    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 814
Number of extensions: 46
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 536
Length of database: 560
Length adjustment: 36
Effective length of query: 500
Effective length of database: 524
Effective search space:   262000
Effective search space used:   262000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)

Align candidate WP_011022927.1 MA_RS15665 (anthranilate synthase component I)
to HMM TIGR01820 (trpE: anthranilate synthase component I (EC 4.1.3.27))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01820.hmm
# target sequence database:        /tmp/gapView.3275186.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01820  [M=449]
Accession:   TIGR01820
Description: TrpE-arch: anthranilate synthase component I
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-212  691.9   0.0   3.1e-212  691.7   0.0    1.0  1  NCBI__GCF_000007345.1:WP_011022927.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007345.1:WP_011022927.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.7   0.0  3.1e-212  3.1e-212       1     449 []      39     553 ..      39     553 .. 0.97

  Alignments for each domain:
  == domain 1  score: 691.7 bits;  conditional E-value: 3.1e-212
                             TIGR01820   1 Plelykalrk..eseysflLesvekqskkaryslvgaspeavvkiner.........kavelfeeivskvkkl 62 
                                           Plely alr   +++ys+lLesvekq+++arys+vg++p+av+kin+r         ka+ lfe+i++k++++
  NCBI__GCF_000007345.1:WP_011022927.1  39 PLELYGALRGsgTTGYSYLLESVEKQESRARYSFVGNDPDAVLKINDRkislellnpKASPLFEAICTKMEEV 111
                                           99*******977888********************************************************** PP

                             TIGR01820  63 eg.......kkkae................gkdvldalrkalkklkeiellee...erqtflGglvGyvaYda 109
                                           +g       +   e                gkdv+dalr a++++++iell++   +rqtflGg++Gy+aYda
  NCBI__GCF_000007345.1:WP_011022927.1 112 CGpetaekeN---EskknagpekftaaiprGKDVFDALRLAFPPANGIELLNSrrfARQTFLGGAIGYTAYDA 181
                                           **76654430...1556678999***************************99988899*************** PP

                             TIGR01820 110 vrdywedaekekeseipeaefllvtkvlvfdhleeevslvvteevsad............eaekiveklkeae 170
                                           ++d+w+++ek +es+ip++++llv+k++v+dhl+eev++v t++vs+             eae++++++k+a+
  NCBI__GCF_000007345.1:WP_011022927.1 182 IYDSWLGVEKGFESDIPDLQYLLVSKSFVLDHLTEEVYIVLTPFVSPGsdaeqvyeealsEAERFYSVIKKAT 254
                                           **********************************************9999*********************** PP

                             TIGR01820 171 keeeekkeaeleslaekee....................feeavekakekifeGdifqvvlSrklelrldldp 223
                                           ++e+++k+ae   +++++                     fee+v +ake+if+GdifqvvlSrk+e++++++p
  NCBI__GCF_000007345.1:WP_011022927.1 255 QPEDAAKAAEGIIASGTDVsgpakapnsnvqvcsvdrsgFEESVLQAKEHIFAGDIFQVVLSRKCEFKMEQSP 327
                                           *********999999855567788889999999999999********************************** PP

                             TIGR01820 224 lelYaklreiNPSPYmyllefgdraivGaSPEtlvrvekrtveinPiAGtapRgkseeeDeelakelLsdeKe 296
                                           +elY +lr+iNPSPYmy++efgd+aivGaSPEtl++v+krtv+inPiAGt+pRgkse+eDe+la+++L+deKe
  NCBI__GCF_000007345.1:WP_011022927.1 328 FELYIQLRAINPSPYMYIFEFGDLAIVGASPETLLTVHKRTVIINPIAGTCPRGKSEAEDETLASHMLNDEKE 400
                                           ************************************************************************* PP

                             TIGR01820 297 rAEHvmLvDLaRNDvrkvsesgsvkvsefmkvlkyshvqHieSevvgtLkkeadafdalkAvfPAGtlsGaPK 369
                                           rAEHvmLvDL+RNDvr+vsesgsvkvs+fmkvlkyshvqHieS+v+gtL++e+d+fda++AvfPAGtlsGaPK
  NCBI__GCF_000007345.1:WP_011022927.1 401 RAEHVMLVDLGRNDVRMVSESGSVKVSGFMKVLKYSHVQHIESTVSGTLRPECDQFDAFRAVFPAGTLSGAPK 473
                                           ************************************************************************* PP

                             TIGR01820 370 irAmeiieelEkepRgvYgGgvGyfslngdadlAiviRtaliekkklriqaGAGivaDSdPekEfeEterKmk 442
                                           irAmeii+e E++pRg+YgGgvGy+s+ngdad+AiviRt+li+++k+++qaGAGivaDSdP++Ef+Et+rKm+
  NCBI__GCF_000007345.1:WP_011022927.1 474 IRAMEIISEREAVPRGIYGGGVGYYSWNGDADFAIVIRTLLIQGRKASVQAGAGIVADSDPAYEFRETDRKMA 546
                                           ************************************************************************* PP

                             TIGR01820 443 avlkaig 449
                                           a+l+aig
  NCBI__GCF_000007345.1:WP_011022927.1 547 AMLTAIG 553
                                           *****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (449 nodes)
Target sequences:                          1  (560 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.89
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis