Alignments for a candidate for trpE in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Thiohalomonas denitrificans HLD2

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_092996656.1 BLP65_RS10660 anthranilate synthase component I

Query= BRENDA::P20580
         (492 letters)



>NCBI__GCF_900102855.1:WP_092996656.1
          Length = 490

 Score =  660 bits (1702), Expect = 0.0
 Identities = 337/490 (68%), Positives = 392/490 (80%), Gaps = 6/490 (1%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60
           M  E F RLAA+GYNRIP+  E LAD DTPLS YLKLAD P +YL ESVQGGEKWGRYSI
Sbjct: 1   MTPEYFARLAAEGYNRIPVMREVLADLDTPLSTYLKLADGPYTYLFESVQGGEKWGRYSI 60

Query: 61  IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120
           IGLPCRTVL+V+ H + +   G   E+    DPLA++E+F+ RY +  VPGLPRF GGLV
Sbjct: 61  IGLPCRTVLKVFGHDIVVEEGGRPVEQATADDPLAWIEDFQGRYHMAEVPGLPRFTGGLV 120

Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180
           GYFGYD VRYVE RL   PN DPLGNPDILLMVSD VVVFDNL+GK++ IV ADP+   A
Sbjct: 121 GYFGYDTVRYVEPRLGDSPNSDPLGNPDILLMVSDEVVVFDNLSGKLYVIVHADPTAGGA 180

Query: 181 YERGQARLEELLERLRQPITP--RRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYIL 238
            ER Q RL+ L+ER+R  ITP  R G+  E     E  F + FT+E +E AV R ++YI 
Sbjct: 181 LERAQQRLDRLVERMRA-ITPVQRSGISTEVT---EKDFVSGFTQEGFEAAVARAREYIA 236

Query: 239 AGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVED 298
           AGD MQVV SQR+SI + A P+DLYRALR  NP+PYMY+ +   F VVGSSPE+LVR ED
Sbjct: 237 AGDIMQVVLSQRLSIPYHARPLDLYRALRSLNPSPYMYYLDLEGFQVVGSSPEILVRAED 296

Query: 299 GLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKV 358
           G VTVRPIAGTRPRG +EE D ALEQ+LL+D KE+AEHLMLIDLGRNDVGR+++ G+V++
Sbjct: 297 GKVTVRPIAGTRPRGKSEEEDRALEQELLADPKELAEHLMLIDLGRNDVGRIAETGSVQL 356

Query: 359 TEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPV 418
           T+KMVIERYS+VMHIVSNV   LR+GL+AMDALRA  PAGT+SGAPKIRAMEIIDELEPV
Sbjct: 357 TDKMVIERYSHVMHIVSNVVADLRDGLTAMDALRATFPAGTVSGAPKIRAMEIIDELEPV 416

Query: 419 KRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRR 478
           KRGVY GAVGYL WNGNMDTAIAIRTAVIK+ +LH+QAG GIV DSVP+ EWEET+NK R
Sbjct: 417 KRGVYSGAVGYLGWNGNMDTAIAIRTAVIKDEKLHIQAGAGIVYDSVPSKEWEETMNKGR 476

Query: 479 AMFRAVALAE 488
           A+FRAVA+AE
Sbjct: 477 AIFRAVAMAE 486


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: 757
Number of extensions: 21
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: 490
Length adjustment: 34
Effective length of query: 458
Effective length of database: 456
Effective search space:   208848
Effective search space used:   208848
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_092996656.1 BLP65_RS10660 (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.4133278.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-179  581.8   0.0   6.3e-179  581.6   0.0    1.0  1  NCBI__GCF_900102855.1:WP_092996656.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900102855.1:WP_092996656.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.6   0.0  6.3e-179  6.3e-179       2     454 ..      26     482 ..      25     483 .. 0.93

  Alignments for each domain:
  == domain 1  score: 581.6 bits;  conditional E-value: 6.3e-179
                             TIGR00564   2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelr 73 
                                           d  tp+s ylkla  ++++l+Esv+ +e++gRyS+igl  ++++k+ ++++v  e   + ++ + +d+l  ++
  NCBI__GCF_900102855.1:WP_092996656.1  26 DLDTPLSTYLKLADGPYTYLFESVQGGEKWGRYSIIGLPCRTVLKVFGHDIVVEEGGRPVEQaTADDPLAWIE 98 
                                           778**********99********************************99665555444444347788888888 PP

                             TIGR00564  74 klleka.eesedeldeplsggavGylgydtvrlveklke.ea.edelelpdlllllvetvivfDhvekkvili 143
                                           ++  ++ + + ++l+  ++gg+vGy+gydtvr+ve+    ++ +d+l  pd+ll++ ++v+vfD+ + k+++i
  NCBI__GCF_900102855.1:WP_092996656.1  99 DFQGRYhMAEVPGLPR-FTGGLVGYFGYDTVRYVEPRLGdSPnSDPLGNPDILLMVSDEVVVFDNLSGKLYVI 170
                                           8888876667777776.******************865434459***************************** PP

                             TIGR00564 144 enarteaersaeeeaaarleellaelqkeleka..vkaleekkesftsnvekeeyeekvakakeyikaGdifq 214
                                            +a  +a+  a e a++rl++l+++++  +  +     +e ++++f s +++e +e++va+a+eyi+aGdi+q
  NCBI__GCF_900102855.1:WP_092996656.1 171 VHADPTAGG-ALERAQQRLDRLVERMRAITPVQrsGISTEVTEKDFVSGFTQEGFEAAVARAREYIAAGDIMQ 242
                                           ***999999.8999********99998765544334456777888**************************** PP

                             TIGR00564 215 vvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatke 287
                                           vvlSqrl+ + +a+p++lYr+LR+ NPSpy+yyldle+f++vgsSPE+lv+ ++ +v++rPiAGtr+RG+++e
  NCBI__GCF_900102855.1:WP_092996656.1 243 VVLSQRLSIPYHARPLDLYRALRSLNPSPYMYYLDLEGFQVVGSSPEILVRAEDGKVTVRPIAGTRPRGKSEE 315
                                           ************************************************************************* PP

                             TIGR00564 288 eDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDa 360
                                           eD+ale+eLlad+Ke AEHlmL+DL+RND+g++a++gsv+ ++ + ie+yshvmHivS+V+  l+d+lta+Da
  NCBI__GCF_900102855.1:WP_092996656.1 316 EDRALEQELLADPKELAEHLMLIDLGRNDVGRIAETGSVQLTDKMVIERYSHVMHIVSNVVADLRDGLTAMDA 388
                                           ************************************************************************* PP

                             TIGR00564 361 lraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaD 433
                                           lra++PaGT+sGAPK+rAme+idelE++kRg+Y+Gavgyl+ +g++dtaiaiRt+v+kd+++++qAgaGiV+D
  NCBI__GCF_900102855.1:WP_092996656.1 389 LRATFPAGTVSGAPKIRAMEIIDELEPVKRGVYSGAVGYLGWNGNMDTAIAIRTAVIKDEKLHIQAGAGIVYD 461
                                           ************************************************************************* PP

                             TIGR00564 434 SdpeaEyeEtlnKakallrai 454
                                           S+p++E+eEt+nK +a  ra+
  NCBI__GCF_900102855.1:WP_092996656.1 462 SVPSKEWEETMNKGRAIFRAV 482
                                           ****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (490 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.71
//
[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 2024 update 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 original 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