Alignments for a candidate for trpE in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Desulfuromonas acetexigens

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_092056118.1 BQ4888_RS07910 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_900111775.1:WP_092056118.1
          Length = 493

 Score =  484 bits (1247), Expect = e-141
 Identities = 265/491 (53%), Positives = 332/491 (67%), Gaps = 12/491 (2%)

Query: 4   EEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSMIGL 63
           E+F  LA  G N IP+  E LAD +TP+S + K+ D   S+LLES++GGEKW RYS +G 
Sbjct: 7   EQFASLATQG-NLIPIYREILADMETPVSAFKKIDDGKTSFLLESIEGGEKWARYSFLGS 65

Query: 64  PSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLVGYF 123
               V R  G    +L DG  ++S D  DPLA +++F   Y+   I GLPRF GG VGY 
Sbjct: 66  GPGRVFRSRGKRYEVLEDGRVIQSGDCADPLAELKAFLAPYRPVPIDGLPRFFGGAVGYL 125

Query: 124 GYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLV----DPAEEQ 179
           GYD VR+VE+      NP  +G  D   ++++ +++FDN+  K+  +  V    D   E 
Sbjct: 126 GYDMVRFVEEL--PDANPARIGAFDSCFLLTEKLLIFDNMRQKIKVVCNVHLAPDADIEA 183

Query: 180 AFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILA 239
           A+ QG A++  L+E LR P+ PR   ++S      P   S YTRE +  AV R KEYI A
Sbjct: 184 AYRQGVAQIDKLIEQLRAPL-PRHAPEIS---TESPVMESDYTREGFMAAVERCKEYIRA 239

Query: 240 GDCMQVVPSQRMSIDFKAA-PIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVED 298
           GD +QVV SQR S    A  P D+YRALR  NP+PYM+F  FGD  VVG+SPEVLVR E 
Sbjct: 240 GDIIQVVLSQRFSGPLGATDPFDIYRALRTINPSPYMFFLRFGDTLVVGASPEVLVRKEG 299

Query: 299 NLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRL 358
           + V VRPIAGTRPRG T E D  LE++LL+D KE AEH+ML+DLGRND+GRVS TGSV +
Sbjct: 300 DQVEVRPIAGTRPRGMTAEQDLVLEEELLADPKERAEHIMLVDLGRNDLGRVSRTGSVEV 359

Query: 359 TEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPV 418
           +E MVIERYS+VMHIVSNV G L EG  A D  RA  PAGTLSGAPKIRAMEIIDELEP 
Sbjct: 360 SELMVIERYSHVMHIVSNVRGHLLEGRDAFDVFRATFPAGTLSGAPKIRAMEIIDELEPC 419

Query: 419 KRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRR 478
           +R +YGGAVGYF+++GNMD AIAIRT VI DG +H+QAG GIVADS P  E++ET+NK +
Sbjct: 420 RREIYGGAVGYFSFSGNMDMAIAIRTLVIRDGRIHLQAGAGIVADSDPDTEYQETVNKAQ 479

Query: 479 AMFRAVALAEQ 489
               A+ +A +
Sbjct: 480 GAMSAITMARK 490


Lambda     K      H
   0.320    0.138    0.403 

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: 689
Number of extensions: 33
Number of successful extensions: 5
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: 493
Length of database: 493
Length adjustment: 34
Effective length of query: 459
Effective length of database: 459
Effective search space:   210681
Effective search space used:   210681
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_092056118.1 BQ4888_RS07910 (anthranilate synthase component I)
to HMM TIGR00564 (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/TIGR00564.hmm
# target sequence database:        /tmp/gapView.7333.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00564  [M=455]
Accession:   TIGR00564
Description: trpE_most: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-175  571.0   0.0   1.2e-175  570.8   0.0    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092056118.1  BQ4888_RS07910 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092056118.1  BQ4888_RS07910 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.8   0.0  1.2e-175  1.2e-175       1     454 [.      27     485 ..      27     486 .. 0.96

  Alignments for each domain:
  == domain 1  score: 570.8 bits;  conditional E-value: 1.2e-175
                                 TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak..ieed 67 
                                               ad +tp+s+++k++  k+sfllEs+e +e+++RyS++g  p  +++ ++++ + le d++ ++    +d
  lcl|NCBI__GCF_900111775.1:WP_092056118.1  27 ADMETPVSAFKKIDDGKTSFLLESIEGGEKWARYSFLGSGPGRVFRSRGKRYEVLE-DGRVIQsgDCAD 94 
                                               5899**********99********************************98555554.44433334899* PP

                                 TIGR00564  68 elkelrklleka.eesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDh 135
                                               +l el+++l+ +    +d+l+  + ggavGylgyd+vr+ve+l+++++ ++   d ++ll+e++++fD+
  lcl|NCBI__GCF_900111775.1:WP_092056118.1  95 PLAELKAFLAPYrPVPIDGLPR-FFGGAVGYLGYDMVRFVEELPDANPARIGAFDSCFLLTEKLLIFDN 162
                                               *********9998889999998.99******************************************** PP

                                 TIGR00564 136 vekkvilienarteaers...aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekva 201
                                               +++k+ ++ n++ + + +   a+++  a++++l+++l+ +l +++++  +++  ++s++++e ++++v+
  lcl|NCBI__GCF_900111775.1:WP_092056118.1 163 MRQKIKVVCNVHLAPDADieaAYRQGVAQIDKLIEQLRAPLPRHAPEISTESPVMESDYTREGFMAAVE 231
                                               **********9988888777899999****************999999999999*************** PP

                                 TIGR00564 202 kakeyikaGdifqvvlSqrleakveak.pfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgk 269
                                               + keyi+aGdi+qvvlSqr++ ++ a+ pf++Yr+LRt+NPSpy+++l + d+ +vg+SPE+lv+ +g+
  lcl|NCBI__GCF_900111775.1:WP_092056118.1 232 RCKEYIRAGDIIQVVLSQRFSGPLGATdPFDIYRALRTINPSPYMFFLRFGDTLVVGASPEVLVRKEGD 300
                                               ***********************97644***************************************** PP

                                 TIGR00564 270 rvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekys 338
                                               +ve+rPiAGtr+RG t e+D +leeeLlad+KerAEH+mLvDL+RND+g+v+++gsvev+el+ ie+ys
  lcl|NCBI__GCF_900111775.1:WP_092056118.1 301 QVEVRPIAGTRPRGMTAEQDLVLEEELLADPKERAEHIMLVDLGRNDLGRVSRTGSVEVSELMVIERYS 369
                                               ********************************************************************* PP

                                 TIGR00564 339 hvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvd 407
                                               hvmHivS+V+G+l ++ +a+D++ra++PaGTlsGAPK+rAme+idelE+ +R+iYgGavgy+sf g++d
  lcl|NCBI__GCF_900111775.1:WP_092056118.1 370 HVMHIVSNVRGHLLEGRDAFDVFRATFPAGTLSGAPKIRAMEIIDELEPCRREIYGGAVGYFSFSGNMD 438
                                               ********************************************************************* PP

                                 TIGR00564 408 taiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               +aiaiRt+v++dg++++qAgaGiVaDSdp++Ey+Et+nKa++ ++ai
  lcl|NCBI__GCF_900111775.1:WP_092056118.1 439 MAIAIRTLVIRDGRIHLQAGAGIVADSDPDTEYQETVNKAQGAMSAI 485
                                               *****************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (493 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.00
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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