Alignments for a candidate for trpE in Thiomicrospira pelophila DSM 1534

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Thiomicrospira pelophila DSM 1534

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_029936187.1 N746_RS0109875 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000711195.1:WP_029936187.1
          Length = 504

 Score =  586 bits (1510), Expect = e-172
 Identities = 300/490 (61%), Positives = 376/490 (76%), Gaps = 2/490 (0%)

Query: 3   REEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSIIG 62
           +  F  LA  GY+  P+    LADF+TPLS+Y KLA+AP SYL ESVQGG+KWGRYSIIG
Sbjct: 6   QSHFDDLAKQGYSHAPVMRTLLADFETPLSVYYKLANAPYSYLFESVQGGDKWGRYSIIG 65

Query: 63  LPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGY 122
           LP  T +RV   QVR+   G   E    ADPLA++E ++A+++V     LP+F GGLVGY
Sbjct: 66  LPSDTHIRVDGQQVRVLRAGEVVEHQVAADPLAWLEAYQAQFKVLDSAELPKFCGGLVGY 125

Query: 123 FGYDCVRYVEKRLATC-PNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENAY 181
           FGYD VRYVE RLA   P  D +G PDILLMVS  +VVFDNL+G++H I+ AD S+ NA+
Sbjct: 126 FGYDTVRYVEPRLAQSQPARDEIGTPDILLMVSRELVVFDNLSGQVHVIIQADLSKPNAF 185

Query: 182 ERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGD 241
           ++ Q R++EL ++L Q          ++ Q  E  F++SF  + +++AV ++K+YIL+GD
Sbjct: 186 KQAQMRIDELEQQLGQSFEKPDSFAADS-QVDEADFKSSFGEQAFKDAVDKVKEYILSGD 244

Query: 242 CMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLV 301
            MQVV SQ+MSIEFK + +DLYRALR  NP+PYM++ N  DF +VGSSPE+LVR+ED LV
Sbjct: 245 AMQVVLSQQMSIEFKQSSLDLYRALRYLNPSPYMFYLNLDDFQIVGSSPEILVRLEDDLV 304

Query: 302 TVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEK 361
           TVRPIAGTR RG + E D ALEQDLL+D KE+AEHLMLIDLGRNDVGR++++G+VK+TEK
Sbjct: 305 TVRPIAGTRRRGTDVEKDRALEQDLLNDPKEVAEHLMLIDLGRNDVGRIAEVGSVKLTEK 364

Query: 362 MVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRG 421
           M++ERYS+VMHIVSNV G L+ GLS ++ LRA  PAGT+SGAPKIRAM+IIDELEPVKRG
Sbjct: 365 MIVERYSHVMHIVSNVDGTLKPGLSPLEVLRATFPAGTVSGAPKIRAMQIIDELEPVKRG 424

Query: 422 VYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMF 481
           VY GAVGYL W+GNMDTAIAIRTAV+KN  L+VQAG GIVADSVP  EW+ET+NK RA+F
Sbjct: 425 VYAGAVGYLGWHGNMDTAIAIRTAVVKNDRLYVQAGAGIVADSVPQSEWDETMNKGRAVF 484

Query: 482 RAVALAEQSV 491
           RA     Q +
Sbjct: 485 RAAEFVSQGL 494


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: 694
Number of extensions: 22
Number of successful extensions: 4
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: 504
Length adjustment: 34
Effective length of query: 458
Effective length of database: 470
Effective search space:   215260
Effective search space used:   215260
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_029936187.1 N746_RS0109875 (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.13940.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-175  570.3   0.0     2e-175  570.1   0.0    1.0  1  lcl|NCBI__GCF_000711195.1:WP_029936187.1  N746_RS0109875 anthranilate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711195.1:WP_029936187.1  N746_RS0109875 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.1   0.0    2e-175    2e-175       2     454 ..      29     487 ..      28     488 .. 0.94

  Alignments for each domain:
  == domain 1  score: 570.1 bits;  conditional E-value: 2e-175
                                 TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedel 69 
                                               d +tp+svy kla+ ++s+l+Esv+ ++++gRyS+igl ++++i++ ++++  l+a +  ++ + +d+l
  lcl|NCBI__GCF_000711195.1:WP_029936187.1  29 DFETPLSVYYKLANAPYSYLFESVQGGDKWGRYSIIGLPSDTHIRVDGQQVRVLRAGEVVEHqVAADPL 97 
                                               789********************************************9988888877765554788999 PP

                                 TIGR00564  70 kelrklleka.eesedeldeplsggavGylgydtvrlveklke..ea.edelelpdlllllvetvivfD 134
                                                 l++  +++   ++ el++ ++gg+vGy+gydtvr+ve+  +  ++ +de+ +pd+ll++ ++++vfD
  lcl|NCBI__GCF_000711195.1:WP_029936187.1  98 AWLEAYQAQFkVLDSAELPK-FCGGLVGYFGYDTVRYVEPRLAqsQPaRDEIGTPDILLMVSRELVVFD 165
                                               99999999995556667776.******************8755343359******************** PP

                                 TIGR00564 135 hvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkes...ftsnvekeeyeekv 200
                                               + + +v++i +a  ++ + a+++a+ r++el ++l ++ ek  ++  +++++   f+s++ +++++++v
  lcl|NCBI__GCF_000711195.1:WP_029936187.1 166 NLSGQVHVIIQADLSKPN-AFKQAQMRIDELEQQLGQSFEKPDSFAADSQVDeadFKSSFGEQAFKDAV 233
                                               *********999777666.9***************99999885555444444444************** PP

                                 TIGR00564 201 akakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgk 269
                                               +k+keyi +Gd +qvvlSq+++ ++++++++lYr+LR  NPSpy++yl+l+df++vgsSPE+lv+++++
  lcl|NCBI__GCF_000711195.1:WP_029936187.1 234 DKVKEYILSGDAMQVVLSQQMSIEFKQSSLDLYRALRYLNPSPYMFYLNLDDFQIVGSSPEILVRLEDD 302
                                               *******************************************************************99 PP

                                 TIGR00564 270 rvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekys 338
                                                v++rPiAGtr+RG + e+D+ale++Ll+d+Ke+AEHlmL+DL+RND+g++a++gsv+ +e + +e+ys
  lcl|NCBI__GCF_000711195.1:WP_029936187.1 303 LVTVRPIAGTRRRGTDVEKDRALEQDLLNDPKEVAEHLMLIDLGRNDVGRIAEVGSVKLTEKMIVERYS 371
                                               9******************************************************************** PP

                                 TIGR00564 339 hvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvd 407
                                               hvmHivS+V G+lk++l+++++lra++PaGT+sGAPK+rAm++idelE++kRg+Y+Gavgyl+ +g++d
  lcl|NCBI__GCF_000711195.1:WP_029936187.1 372 HVMHIVSNVDGTLKPGLSPLEVLRATFPAGTVSGAPKIRAMQIIDELEPVKRGVYAGAVGYLGWHGNMD 440
                                               ********************************************************************* PP

                                 TIGR00564 408 taiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               taiaiRt+v+k++++yvqAgaGiVaDS+p++E++Et+nK +a+ ra+
  lcl|NCBI__GCF_000711195.1:WP_029936187.1 441 TAIAIRTAVVKNDRLYVQAGAGIVADSVPQSEWDETMNKGRAVFRAA 487
                                               ******************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (504 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: 8.22
//
[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