Alignments for a candidate for trpE in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Acidovorax sp. GW101-3H11

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate Ac3H11_767 Anthranilate synthase, aminase component (EC 4.1.3.27)

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_767
          Length = 499

 Score =  523 bits (1346), Expect = e-153
 Identities = 277/502 (55%), Positives = 356/502 (70%), Gaps = 22/502 (4%)

Query: 5   EFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPN----SYLLESVQGGEKWGRYSI 60
           EF  LA++GYNRIPL  E  AD +TPLS+YLKLA   +    S+LLESV GGE++GRYS 
Sbjct: 6   EFKSLASEGYNRIPLMAEAFADLETPLSLYLKLAHTKDGGKHSFLLESVVGGERFGRYSF 65

Query: 61  IGLPCRTVLRVY----DHQVRISIDG--VETERFDCADPLAFVEEFKARYQVPTVPGLPR 114
           IGLP RT+LR      D +  +  DG  VET +    +PL F+ +++ R++V   PGLPR
Sbjct: 66  IGLPARTLLRASGFGADARTEVVTDGQVVETAQ---GNPLDFIADYQKRFKVALRPGLPR 122

Query: 115 FDGGLVGYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLAD 174
           F GGL GYFGYD VRY+EK+L T   PD LG PDILL+  + + V DNL+GK++ IV AD
Sbjct: 123 FCGGLAGYFGYDAVRYIEKKLETTCPPDTLGCPDILLLQCEELAVIDNLSGKLYLIVYAD 182

Query: 175 PSEENAYERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIK 234
           P++  AY R + RL EL E+L+  ++      +  A    PA R  F + DY  AV R K
Sbjct: 183 PAQPEAYTRAKKRLRELKEQLKYSVSA----PVVKATESHPAQR-DFAKADYLAAVHRAK 237

Query: 235 DYILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLV 294
           + I AGD MQV   QR+   +  +P+ LYRALR  NP+PYMYF++FGDFHVVG+SPE+LV
Sbjct: 238 ELIAAGDFMQVQVGQRIHKRYTESPLSLYRALRSLNPSPYMYFYDFGDFHVVGASPEILV 297

Query: 295 R---VEDGL-VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRV 350
           R    E+G  VT+RP+AGTRPRG   E D A E +L++D KE AEH+MLIDL RND+GR+
Sbjct: 298 RQEKTEEGTKVTIRPLAGTRPRGATPEKDKATEVELINDPKERAEHVMLIDLARNDIGRI 357

Query: 351 SDIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAME 410
           +  G VKVTE   +ERYS+VMHIVSNV G L +G+++MD L+A  PAGTL+GAPK+ AME
Sbjct: 358 AKTGTVKVTEAFAVERYSHVMHIVSNVEGILNDGMTSMDVLKATFPAGTLTGAPKVHAME 417

Query: 411 IIDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEW 470
           +ID+LEP KRG+YGGA GYL++ G+MD AIAIRT +IKNG L+VQA  G+VADSVP LEW
Sbjct: 418 LIDQLEPTKRGLYGGACGYLSYAGDMDVAIAIRTGIIKNGTLYVQAAAGVVADSVPELEW 477

Query: 471 EETINKRRAMFRAVALAEQSVE 492
           +ET +K RA+ RA  L E+ +E
Sbjct: 478 KETEHKARALLRAAELVEEGLE 499


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: 659
Number of extensions: 33
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: 499
Length adjustment: 34
Effective length of query: 458
Effective length of database: 465
Effective search space:   212970
Effective search space used:   212970
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 Ac3H11_767 (Anthranilate synthase, aminase component (EC 4.1.3.27))
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.26656.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     5e-165  535.8   0.0   5.7e-165  535.6   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767  Anthranilate synthase, aminase c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767  Anthranilate synthase, aminase component (EC 4.1.3.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.6   0.0  5.7e-165  5.7e-165       1     454 [.      26     491 ..      26     492 .. 0.92

  Alignments for each domain:
  == domain 1  score: 535.6 bits;  conditional E-value: 5.7e-165
                                       TIGR00564   1 adtltpisvylklak.r...kesfllEsvekeeelgRySliglnpvleikakdg...kavlle 56 
                                                     ad +tp+s+ylkla+ +   k+sfllEsv  +e+ gRyS+igl  ++ ++a++      +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767  26 ADLETPLSLYLKLAHtKdggKHSFLLESVVGGERFGRYSFIGLPARTLLRASGFgadARTEVV 88 
                                                     5889**********9647999**********************99998888764333334444 PP

                                       TIGR00564  57 addeeak.ieedelkelrklleka.eesedeldeplsggavGylgydtvrlveklkeea..ed 115
                                                     +d++  +  ++++l+ + +  +++    +++l+  ++gg+ Gy+gyd vr++ek+ e++  +d
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767  89 TDGQVVEtAQGNPLDFIADYQKRFkVALRPGLPR-FCGGLAGYFGYDAVRYIEKKLETTcpPD 150
                                                     45554446899************95556777776.*******************9885446** PP

                                       TIGR00564 116 elelpdlllllvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavk 178
                                                     +l  pd+lll +e+++v D+ + k++li +a  ++ + a++ a++rl+el ++l+ +++  v 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767 151 TLGCPDILLLQCEELAVIDNLSGKLYLIVYADPAQPE-AYTRAKKRLRELKEQLKYSVSAPV- 211
                                                     *******************************777666.9999*************9998543. PP

                                       TIGR00564 179 aleekkesftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNP 241
                                                     ++ +++++ + ++ k++y ++v++ake i+aGd++qv++ qr++++ + +p++lYr+LR+ NP
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767 212 VKATESHPAQRDFAKADYLAAVHRAKELIAAGDFMQVQVGQRIHKRYTESPLSLYRALRSLNP 274
                                                     345556668899*************************************************** PP

                                       TIGR00564 242 SpylyyldledfelvgsSPEllvkvk....gkrvetrPiAGtrkRGatkeeDealeeeLlade 300
                                                     Spy+y+ d+ df++vg+SPE+lv+ +    g +v++rP+AGtr+RGat+e+D+a e eL++d+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767 275 SPYMYFYDFGDFHVVGASPEILVRQEkteeGTKVTIRPLAGTRPRGATPEKDKATEVELINDP 337
                                                     ***********************9887766667****************************** PP

                                       TIGR00564 301 KerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalra 363
                                                     KerAEH+mL+DLaRNDig++ak+g+v+v+e + +e+yshvmHivS+VeG l+d++t++D+l+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767 338 KERAEHVMLIDLARNDIGRIAKTGTVKVTEAFAVERYSHVMHIVSNVEGILNDGMTSMDVLKA 400
                                                     *************************************************************** PP

                                       TIGR00564 364 alPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqA 426
                                                     ++PaGTl+GAPKv+Amelid+lE++kRg+YgGa gyls++gd+d+aiaiRt ++k+g++yvqA
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767 401 TFPAGTLTGAPKVHAMELIDQLEPTKRGLYGGACGYLSYAGDMDVAIAIRTGIIKNGTLYVQA 463
                                                     *************************************************************** PP

                                       TIGR00564 427 gaGiVaDSdpeaEyeEtlnKakallrai 454
                                                     +aG+VaDS+pe E++Et +Ka+allra+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_767 464 AAGVVADSVPELEWKETEHKARALLRAA 491
                                                     *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (499 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: 13.16
//
[ok]

This GapMind analysis is from Apr 09 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