Alignments for a candidate for trpE in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Desulfallas geothermicus DSM 3669

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_092481608.1 BM299_RS01080 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_900115975.1:WP_092481608.1
          Length = 492

 Score =  386 bits (992), Expect = e-112
 Identities = 229/493 (46%), Positives = 296/493 (60%), Gaps = 17/493 (3%)

Query: 4   EEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIGL 63
           +E+L L+   YN +P+  E  AD +TP++++LKLA    S LLESV+GG   GRYS I L
Sbjct: 7   QEYLSLSRQ-YNLVPVFTECHADTETPITLFLKLAGRGPSCLLESVEGGRYLGRYSFIAL 65

Query: 64  PCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYF 123
                 R  D +  ++  G      D   PL  + +  + ++VP +  LPRF GG VG+ 
Sbjct: 66  DPLLTFRSRDGRGEVAHCGGVVRVAD-GPPLETLGKLLSSFRVPEMTQLPRFYGGAVGFV 124

Query: 124 GYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVL-----ADPSEE 178
            YD VR +E    T    D L  PD L      VV+FD++   +  +V       DP+  
Sbjct: 125 AYDAVRSLEDLPGT--PADELHMPDCLQFFPGTVVIFDHVRHNVTFVVNIPQDGTDPAV- 181

Query: 179 NAYERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYIL 238
             YER   +LE +   LR+P+       L  A        A     ++   VGR  +YI 
Sbjct: 182 -LYERAARKLETMRAALRKPLPVSSQFSLRGA------IMADLPEHEFRQRVGRALEYIR 234

Query: 239 AGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVED 298
           +G+ +QVV S+R ++ F      +YR LR  NP+PYMY+ N GD  V+GSSPE+LVR+E+
Sbjct: 235 SGEIIQVVLSRRFAVGFHGDDFAVYRRLRSVNPSPYMYYLNLGDIKVIGSSPEMLVRMEN 294

Query: 299 GLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKV 358
           G VT  PIAGTRPRG +   D  L  +LL+D KE AEHLML+DLGRND+GRV   G V+V
Sbjct: 295 GRVTTCPIAGTRPRGDSPAEDGRLADELLADEKERAEHLMLVDLGRNDLGRVCVPGTVQV 354

Query: 359 TEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPV 418
              M IE +S+VMHIVS V G L  G  A+DAL A  PAGT+SGAPK+RAMEIIDELEP 
Sbjct: 355 PRFMDIEYFSHVMHIVSRVEGDLAPGADALDALAACFPAGTVSGAPKVRAMEIIDELEPC 414

Query: 419 KRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRR 478
           +RGVY GAVGYL +NGNMDTAIAIRT VIK    ++QAG GIVADS P  E  E  +K R
Sbjct: 415 RRGVYAGAVGYLGFNGNMDTAIAIRTLVIKGNTAYIQAGAGIVADSDPLRESREIASKAR 474

Query: 479 AMFRAVALAEQSV 491
           AMF  + + E+ V
Sbjct: 475 AMFSTLGVEEKRV 487


Lambda     K      H
   0.321    0.139    0.408 

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: 638
Number of extensions: 37
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: 492
Length of database: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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_092481608.1 BM299_RS01080 (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.7219.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-169  550.3   0.0   2.3e-169  550.1   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092481608.1  BM299_RS01080 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092481608.1  BM299_RS01080 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.1   0.0  2.3e-169  2.3e-169       1     453 [.      27     479 ..      27     481 .. 0.96

  Alignments for each domain:
  == domain 1  score: 550.1 bits;  conditional E-value: 2.3e-169
                                 TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedel 69 
                                               adt+tpi+++lkla r  s+llEsve +  lgRyS+i+l+p l+++ +dg+ + ++  +     ++ +l
  lcl|NCBI__GCF_900115975.1:WP_092481608.1  27 ADTETPITLFLKLAGRGPSCLLESVEGGRYLGRYSFIALDPLLTFRSRDGRGEVAHCGGVVRVADGPPL 95 
                                               699***********************************************877777777777789**** PP

                                 TIGR00564  70 kelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvek 138
                                               ++l kll++++  e+ + + ++ggavG+++yd vr++e+l+ ++ del++pd+l ++  tv++fDhv++
  lcl|NCBI__GCF_900115975.1:WP_092481608.1  96 ETLGKLLSSFRVPEMTQLPRFYGGAVGFVAYDAVRSLEDLPGTPADELHMPDCLQFFPGTVVIFDHVRH 164
                                               *********98777777788************************************************* PP

                                 TIGR00564 139 kvilienarteaers...aeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakak 204
                                               +v+++ n+  +++++    +e aa++le++ a l+k+l   v+ ++  +  +++++ ++e+ ++v +a 
  lcl|NCBI__GCF_900115975.1:WP_092481608.1 165 NVTFVVNI-PQDGTDpavLYERAARKLETMRAALRKPLP--VSSQFSLRGAIMADLPEHEFRQRVGRAL 230
                                               ******99.6667776777889999************96..788899999999**************** PP

                                 TIGR00564 205 eyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvet 273
                                               eyi++G+i+qvvlS+r+++ ++ + f++Yr+LR+vNPSpy+yyl+l d++++gsSPE+lv++++ rv+t
  lcl|NCBI__GCF_900115975.1:WP_092481608.1 231 EYIRSGEIIQVVLSRRFAVGFHGDDFAVYRRLRSVNPSPYMYYLNLGDIKVIGSSPEMLVRMENGRVTT 299
                                               ***************************************************************99**** PP

                                 TIGR00564 274 rPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmH 342
                                                PiAGtr+RG++++eD +l++eLladeKerAEHlmLvDL+RND+g+v+ +g+v+v+++++ie +shvmH
  lcl|NCBI__GCF_900115975.1:WP_092481608.1 300 CPIAGTRPRGDSPAEDGRLADELLADEKERAEHLMLVDLGRNDLGRVCVPGTVQVPRFMDIEYFSHVMH 368
                                               ********************************************************************* PP

                                 TIGR00564 343 ivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaia 411
                                               ivS+VeG l+++++a+Dal a++PaGT+sGAPKvrAme+idelE+ +Rg+Y+Gavgyl+f+g++dtaia
  lcl|NCBI__GCF_900115975.1:WP_092481608.1 369 IVSRVEGDLAPGADALDALAACFPAGTVSGAPKVRAMEIIDELEPCRRGVYAGAVGYLGFNGNMDTAIA 437
                                               ********************************************************************* PP

                                 TIGR00564 412 iRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallra 453
                                               iRt+v+k ++ay+qAgaGiVaDSdp +E +E   Ka+a+ ++
  lcl|NCBI__GCF_900115975.1:WP_092481608.1 438 IRTLVIKGNTAYIQAGAGIVADSDPLRESREIASKARAMFST 479
                                               **************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (492 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.59
//
[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