Alignments for a candidate for trpE in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Hydrogenovibrio marinus DSM 11271

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_029910648.1 P166_RS0107545 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000711315.1:WP_029910648.1
          Length = 501

 Score =  578 bits (1489), Expect = e-169
 Identities = 291/489 (59%), Positives = 369/489 (75%), Gaps = 2/489 (0%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60
           M+   F RLA  GY   P+    L+D++TPLS+Y K+A+QP SYL ESVQGG+KWGRYS+
Sbjct: 1   MSNPHFSRLANQGYKTTPVMHTMLSDYETPLSVYHKVANQPQSYLFESVQGGDKWGRYSI 60

Query: 61  IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120
           IGLP    + V G+ ++++     +E    +DPLA++E+F++R+KV    G+P F+GGLV
Sbjct: 61  IGLPCSKRLIVKGHQITLMDGDAVLEQQVSDDPLAWIEAFQNRFKVYPEAGMPAFSGGLV 120

Query: 121 GYFGYDCVRYVEKRLGVS-PNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQ 179
           GYFGYD VRY+EKRL  S P  D +G PDI+L+VS+ VVVFDNL+G++H IV  D ++  
Sbjct: 121 GYFGYDAVRYMEKRLQNSVPERDDIGAPDIVLLVSEEVVVFDNLSGQLHIIVHADLSQAD 180

Query: 180 AFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILA 239
           A  + Q R+  + + +R  + P            E +F SS+  E+++ AV RIKEYILA
Sbjct: 181 AEAKAQKRISEIADQIRTAM-PVPSEPEPSKLLGEQDFHSSFGEEEFKQAVARIKEYILA 239

Query: 240 GDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDN 299
           GD MQ+V SQ+MS+DF+  P+DLYRALR  NP+PYM+F + G+  +VGSSPE+LVR+EDN
Sbjct: 240 GDAMQIVISQQMSVDFEHEPMDLYRALRHLNPSPYMFFVDLGELQIVGSSPEILVRLEDN 299

Query: 300 LVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLT 359
            VTVRPIAGTR RG T E D+ALE+DLL+D KEIAEHLMLIDLGRNDVGR++  GSV LT
Sbjct: 300 KVTVRPIAGTRRRGTTPERDKALEEDLLADPKEIAEHLMLIDLGRNDVGRIAQVGSVELT 359

Query: 360 EKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVK 419
           EKMV+ERYS+VMHIVSNV G L+ G++ MD LRA  PAGT+SGAPKIRAMEIIDELEPVK
Sbjct: 360 EKMVVERYSHVMHIVSNVNGDLKPGMSPMDVLRATFPAGTVSGAPKIRAMEIIDELEPVK 419

Query: 420 RGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRA 479
           RG+Y GAVGY  W+GNMDTAIAIRTAVI D +L VQAG GIVADSVP  EW+ET+NK RA
Sbjct: 420 RGIYAGAVGYLGWHGNMDTAIAIRTAVIKDKKLFVQAGAGIVADSVPQSEWDETMNKGRA 479

Query: 480 MFRAVALAE 488
           +F+AV   +
Sbjct: 480 VFKAVEFVQ 488


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: 762
Number of extensions: 28
Number of successful extensions: 3
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: 501
Length adjustment: 34
Effective length of query: 459
Effective length of database: 467
Effective search space:   214353
Effective search space used:   214353
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_029910648.1 P166_RS0107545 (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.2661834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-178  577.9   0.0   9.6e-178  577.7   0.0    1.0  1  NCBI__GCF_000711315.1:WP_029910648.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711315.1:WP_029910648.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.7   0.0  9.6e-178  9.6e-178       2     454 ..      26     484 ..      25     485 .. 0.94

  Alignments for each domain:
  == domain 1  score: 577.7 bits;  conditional E-value: 9.6e-178
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelr 73 
                                           d +tp+svy+k+a++++s+l+Esv+ ++++gRyS+igl   +++ +k+++++l++ d   ++ + +d+l  ++
  NCBI__GCF_000711315.1:WP_029910648.1  26 DYETPLSVYHKVANQPQSYLFESVQGGDKWGRYSIIGLPCSKRLIVKGHQITLMDGDAVLEQqVSDDPLAWIE 98 
                                           889**********************************************999988887655547899999999 PP

                             TIGR00564  74 kllekaeesedeldeplsggavGylgydtvrlveklke...eaedelelpdlllllvetvivfDhvekkvili 143
                                           ++ ++++   +   +++sgg+vGy+gyd vr++ek  +   +++d++  pd++ll+ e+v+vfD+ + ++++i
  NCBI__GCF_000711315.1:WP_029910648.1  99 AFQNRFKVYPEAGMPAFSGGLVGYFGYDAVRYMEKRLQnsvPERDDIGAPDIVLLVSEEVVVFDNLSGQLHII 171
                                           9999997666666688******************98774544599**************************99 PP

                             TIGR00564 144 enarteaersaeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeyeekvakakeyikaGdif 213
                                            +a   ++ +ae++a++r++e++ ++++++       + +   +++f+s++ +ee++++va++keyi aGd +
  NCBI__GCF_000711315.1:WP_029910648.1 172 VHADL-SQADAEAKAQKRISEIADQIRTAMPVPsepEPSKLLGEQDFHSSFGEEEFKQAVARIKEYILAGDAM 243
                                           99844.45558999***********999886443345556667778*************************** PP

                             TIGR00564 214 qvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatk 286
                                           q+v+Sq++++++e +p++lYr+LR+ NPSpy++++dl ++++vgsSPE+lv++++++v++rPiAGtr+RG t+
  NCBI__GCF_000711315.1:WP_029910648.1 244 QIVISQQMSVDFEHEPMDLYRALRHLNPSPYMFFVDLGELQIVGSSPEILVRLEDNKVTVRPIAGTRRRGTTP 316
                                           ************************************************************************* PP

                             TIGR00564 287 eeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavD 359
                                           e D+alee+Llad+Ke AEHlmL+DL+RND+g++a++gsve +e + +e+yshvmHivS+V+G lk++++++D
  NCBI__GCF_000711315.1:WP_029910648.1 317 ERDKALEEDLLADPKEIAEHLMLIDLGRNDVGRIAQVGSVELTEKMVVERYSHVMHIVSNVNGDLKPGMSPMD 389
                                           ************************************************************************* PP

                             TIGR00564 360 alraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVa 432
                                           +lra++PaGT+sGAPK+rAme+idelE++kRgiY+Gavgyl+ +g++dtaiaiRt+v+kd++++vqAgaGiVa
  NCBI__GCF_000711315.1:WP_029910648.1 390 VLRATFPAGTVSGAPKIRAMEIIDELEPVKRGIYAGAVGYLGWHGNMDTAIAIRTAVIKDKKLFVQAGAGIVA 462
                                           ************************************************************************* PP

                             TIGR00564 433 DSdpeaEyeEtlnKakallrai 454
                                           DS+p++E++Et+nK +a+ +a+
  NCBI__GCF_000711315.1:WP_029910648.1 463 DSVPQSEWDETMNKGRAVFKAV 484
                                           *****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (501 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.80
//
[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