Alignments for a candidate for trpE in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Teredinibacter turnerae T7901

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_015816820.1 TERTU_RS13865 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_000023025.1:WP_015816820.1
          Length = 492

 Score =  596 bits (1537), Expect = e-175
 Identities = 309/489 (63%), Positives = 367/489 (75%), Gaps = 6/489 (1%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M  E F +LAA G+NRIP+  E LAD +TPLS Y KLA+ P SYL ESVQGGEKWGRYSI
Sbjct: 1   MTPELFSQLAAAGHNRIPVRREVLADTETPLSSYFKLANGPYSYLFESVQGGEKWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLP R  L V ++ V+   +    E  DC DPL FV+ ++  + V  V GLP F+GGLV
Sbjct: 61  IGLPARERLEVRENTVQFFNESGLVESSDCDDPLEFVKNWQKSFNVAEVDGLPSFNGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYF YDCVRYVE RL      D +G P+ILLMVSD ++VFDNL GKIH IVLADP+  NA
Sbjct: 121 GYFAYDCVRYVEPRLQGNAPDDEIGTPEILLMVSDEILVFDNLKGKIHLIVLADPARANA 180

Query: 181 YERGQARLEELLERLRQ-----PITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKD 235
            +    RL+ L  +L       P  P      +     E  F +S+  E ++  VGR+KD
Sbjct: 181 LQLANDRLDALEAKLASGPGNIPAMPAMNTS-KGITACEGDFESSYGCEKFQADVGRLKD 239

Query: 236 YILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVR 295
           YILAGD MQ+V SQRMS  F A P++LYRALRC NP+PYMYF N GD HVVGSSPE+L R
Sbjct: 240 YILAGDTMQIVLSQRMSYPFTAPPVNLYRALRCLNPSPYMYFMNLGDHHVVGSSPEILAR 299

Query: 296 VEDGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGA 355
           +E+G +TVRPIAGTR RG +E  D ALE +L++D KEIAEHLMLIDLGRNDVGRV++IG+
Sbjct: 300 LENGEMTVRPIAGTRRRGYSEAEDKALEAELVADPKEIAEHLMLIDLGRNDVGRVAEIGS 359

Query: 356 VKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDEL 415
           VK+TEKMV+ER+S+VMHI SNVTG+L+    AMD LRA LPAGTLSGAPKIRAMEIIDEL
Sbjct: 360 VKLTEKMVVERFSHVMHITSNVTGRLKADKDAMDVLRAALPAGTLSGAPKIRAMEIIDEL 419

Query: 416 EPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETIN 475
           EPVKRG+YGGA+GYLAWNGNMDTAIAIRTAVIK+G++ VQAG G+VADS P LEW+ET+N
Sbjct: 420 EPVKRGIYGGAIGYLAWNGNMDTAIAIRTAVIKDGKIFVQAGAGVVADSQPELEWKETMN 479

Query: 476 KRRAMFRAV 484
           K RA+F AV
Sbjct: 480 KARALFSAV 488


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: 723
Number of extensions: 28
Number of successful extensions: 2
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_015816820.1 TERTU_RS13865 (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.11741.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-172  560.7   0.0   1.6e-172  560.5   0.0    1.0  1  lcl|NCBI__GCF_000023025.1:WP_015816820.1  TERTU_RS13865 anthranilate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015816820.1  TERTU_RS13865 anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.5   0.0  1.6e-172  1.6e-172       1     454 [.      25     488 ..      25     489 .. 0.92

  Alignments for each domain:
  == domain 1  score: 560.5 bits;  conditional E-value: 1.6e-172
                                 TIGR00564   1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieede 68 
                                               adt+tp+s y kla+ ++s+l+Esv+ +e++gRyS+igl  + ++++++++++ +++++  ++   +d+
  lcl|NCBI__GCF_000023025.1:WP_015816820.1  25 ADTETPLSSYFKLANGPYSYLFESVQGGEKWGRYSIIGLPARERLEVRENTVQFFNESGLVESsDCDDP 93 
                                               699***********99**********************************9999998876665478999 PP

                                 TIGR00564  69 lkelrklleka.eesedeldeplsggavGylgydtvrlveklke.ea.edelelpdlllllvetvivfD 134
                                               l+ ++++ +++   + d+l+  + gg+vGy++yd+vr+ve+  + +a  de+ +p++ll++ ++++vfD
  lcl|NCBI__GCF_000023025.1:WP_015816820.1  94 LEFVKNWQKSFnVAEVDGLPS-FNGGLVGYFAYDCVRYVEPRLQgNApDDEIGTPEILLMVSDEILVFD 161
                                               ******999995556666766.******************98775445999****************** PP

                                 TIGR00564 135 hvekkvilienarteaersaeeeaaarleellaelqkeleka..vkaleekkes.........ftsnve 192
                                               + + k++li  a  +  + a + a++rl++l a+l +   +   ++a+ +   s         f+s++ 
  lcl|NCBI__GCF_000023025.1:WP_015816820.1 162 NLKGKIHLIVLADPARAN-ALQLANDRLDALEAKLASGPGNIpaMPAMNT---SkgitacegdFESSYG 226
                                               ***********9777666.8888899999988888775432111333333...2233566667888888 PP

                                 TIGR00564 193 keeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPE 261
                                                e+++++v ++k+yi aGd +q+vlSqr++ +++a+p++lYr+LR  NPSpy+y+++l d ++vgsSPE
  lcl|NCBI__GCF_000023025.1:WP_015816820.1 227 CEKFQADVGRLKDYILAGDTMQIVLSQRMSYPFTAPPVNLYRALRCLNPSPYMYFMNLGDHHVVGSSPE 295
                                               8******************************************************************** PP

                                 TIGR00564 262 llvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevke 330
                                               +l ++++ ++++rPiAGtr+RG +++eD+ale+eL+ad+Ke AEHlmL+DL+RND+g+va++gsv+ +e
  lcl|NCBI__GCF_000023025.1:WP_015816820.1 296 ILARLENGEMTVRPIAGTRRRGYSEAEDKALEAELVADPKEIAEHLMLIDLGRNDVGRVAEIGSVKLTE 364
                                               ******999************************************************************ PP

                                 TIGR00564 331 llkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgy 399
                                                + +e++shvmHi+S+V+G+lk +++a+D+lraalPaGTlsGAPK+rAme+idelE++kRgiYgGa+gy
  lcl|NCBI__GCF_000023025.1:WP_015816820.1 365 KMVVERFSHVMHITSNVTGRLKADKDAMDVLRAALPAGTLSGAPKIRAMEIIDELEPVKRGIYGGAIGY 433
                                               ********************************************************************* PP

                                 TIGR00564 400 lsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                               l  +g++dtaiaiRt+v+kdg+++vqAgaG+VaDS+pe E++Et+nKa+al +a+
  lcl|NCBI__GCF_000023025.1:WP_015816820.1 434 LAWNGNMDTAIAIRTAVIKDGKIFVQAGAGVVADSQPELEWKETMNKARALFSAV 488
                                               **************************************************99886 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: 00:00:00.02
# Mc/sec: 10.45
//
[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