Alignments for a candidate for trpE in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Burkholderia vietnamiensis G4

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_011883154.1 anthranilate synthase component I

Query= SwissProt::P20579
         (493 letters)



>NCBI__GCF_000016205.1:WP_011883154.1
          Length = 497

 Score =  547 bits (1410), Expect = e-160
 Identities = 282/492 (57%), Positives = 363/492 (73%), Gaps = 16/492 (3%)

Query: 1   MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQP-----NSYLLESVQGGEKW 55
           M   EF  LA  GYNRIPL  E LAD +TPLS+YLKLA QP     NS+LLESV GGE++
Sbjct: 1   MTELEFQSLANEGYNRIPLIAEALADLETPLSLYLKLA-QPERAGANSFLLESVVGGERF 59

Query: 56  GRYSMIGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRF 115
           GRYS IGLP+RT++R       ++ DG  +E+HD  DP AF+ESF+ R+KVA  PGLPRF
Sbjct: 60  GRYSFIGLPARTLVRARNGVSEVVRDGEVIETHD-GDPFAFIESFQARFKVAQRPGLPRF 118

Query: 116 NGGLVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDP 175
            GGL GYFGYD VRY+EK+L  +   D LG+PDI L++++ V V DNLAGK++ I+  DP
Sbjct: 119 CGGLAGYFGYDAVRYIEKKLANTAPRDDLGLPDIQLLLTEEVAVIDNLAGKLYLIIYADP 178

Query: 176 AEEQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKE 235
           A+ +A+ +G+ RL+ L + LR  + P     ++        FR  + +EDY  AV + KE
Sbjct: 179 AQPEAYTKGKQRLRELKQRLRTTVQP----PVTSASVRTETFRE-FKKEDYLAAVRQAKE 233

Query: 236 YILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVR 295
           YI AG+ MQ+   QR++  ++  P+ LYRALR  NP+PYMY++NFGDFHVVG+SPE+LVR
Sbjct: 234 YIAAGELMQIQVGQRLTKPYRDNPLSLYRALRSLNPSPYMYYYNFGDFHVVGASPEILVR 293

Query: 296 VE----DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVS 351
            E    D +VT+RP+AGTRPRG T E D  L  +LL+D KEIAEH+MLIDL RNDVGR++
Sbjct: 294 QEKRGDDQIVTIRPLAGTRPRGNTPERDAELATELLNDPKEIAEHVMLIDLARNDVGRIA 353

Query: 352 STGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEI 411
             GSV++T+KMVIE+YS+V HIVS+V G+L+ G+T  D LRA  PAGTLSGAPK+RAME+
Sbjct: 354 QIGSVQVTDKMVIEKYSHVQHIVSSVEGKLKPGMTNYDVLRATFPAGTLSGAPKVRAMEL 413

Query: 412 IDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWE 471
           IDELEPVKRG+YGGAVGY +++G MD AIAIRT +I++G L+VQA  G+VADSVP  EW+
Sbjct: 414 IDELEPVKRGLYGGAVGYMSFSGEMDLAIAIRTGLIHNGNLYVQAAAGVVADSVPESEWQ 473

Query: 472 ETINKRRAMFRA 483
           ET NK RA+ RA
Sbjct: 474 ETENKARAVLRA 485


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: 702
Number of extensions: 37
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: 493
Length of database: 497
Length adjustment: 34
Effective length of query: 459
Effective length of database: 463
Effective search space:   212517
Effective search space used:   212517
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_011883154.1 (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.17069.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-169  551.0   0.0   1.5e-169  550.8   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011883154.1  anthranilate synthase component 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011883154.1  anthranilate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.8   0.0  1.5e-169  1.5e-169       1     454 [.      25     486 ..      25     487 .. 0.94

  Alignments for each domain:
  == domain 1  score: 550.8 bits;  conditional E-value: 1.5e-169
                                 TIGR00564   1 adtltpisvylklak.r...kesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.i 64 
                                               ad +tp+s+ylkla+ +   ++sfllEsv  +e+ gRyS+igl  ++ ++a++g + ++  d+e ++ +
  lcl|NCBI__GCF_000016205.1:WP_011883154.1  25 ADLETPLSLYLKLAQpEragANSFLLESVVGGERFGRYSFIGLPARTLVRARNG-VSEVVRDGEVIEtH 92 
                                               5889**********97578899*********************99999999987.55555555555548 PP

                                 TIGR00564  65 eedelkelrklleka.eesedeldeplsggavGylgydtvrlveklkeea..edelelpdlllllvetv 130
                                               ++d+   ++++ +++   ++++l+  ++gg+ Gy+gyd vr++ek+ +++  +d+l lpd+ lll+e+v
  lcl|NCBI__GCF_000016205.1:WP_011883154.1  93 DGDPFAFIESFQARFkVAQRPGLPR-FCGGLAGYFGYDAVRYIEKKLANTapRDDLGLPDIQLLLTEEV 160
                                               9*************96667788887.******************998844359**************** PP

                                 TIGR00564 131 ivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeek 199
                                               +v D+ + k++li +a  ++ + a+++ ++rl+el ++l++++++ v+    ++e+f  +++ke+y ++
  lcl|NCBI__GCF_000016205.1:WP_011883154.1 161 AVIDNLAGKLYLIIYADPAQPE-AYTKGKQRLRELKQRLRTTVQPPVTSASVRTETF-REFKKEDYLAA 227
                                               ****************777666.9********************9999888888888.89********* PP

                                 TIGR00564 200 vakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk. 267
                                               v++akeyi+aG+++q+++ qrl+++ + +p++lYr+LR+ NPSpy+yy ++ df++vg+SPE+lv+ + 
  lcl|NCBI__GCF_000016205.1:WP_011883154.1 228 VRQAKEYIAAGELMQIQVGQRLTKPYRDNPLSLYRALRSLNPSPYMYYYNFGDFHVVGASPEILVRQEk 296
                                               ******************************************************************997 PP

                                 TIGR00564 268 ..gkr.vetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellk 333
                                                 +++ v++rP+AGtr+RG+t+e D+ l++eLl+d+Ke AEH+mL+DLaRND+g++a++gsv+v++ + 
  lcl|NCBI__GCF_000016205.1:WP_011883154.1 297 rgDDQiVTIRPLAGTRPRGNTPERDAELATELLNDPKEIAEHVMLIDLARNDVGRIAQIGSVQVTDKMV 365
                                               7645579************************************************************** PP

                                 TIGR00564 334 iekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsf 402
                                               iekyshv+HivS+VeG+lk+++t++D+lra++PaGTlsGAPKvrAmelidelE++kRg+YgGavgy+sf
  lcl|NCBI__GCF_000016205.1:WP_011883154.1 366 IEKYSHVQHIVSSVEGKLKPGMTNYDVLRATFPAGTLSGAPKVRAMELIDELEPVKRGLYGGAVGYMSF 434
                                               ********************************************************************* PP

                                 TIGR00564 403 dgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454
                                                g++d aiaiRt ++++g +yvqA+aG+VaDS+pe+E++Et nKa+a+lra+
  lcl|NCBI__GCF_000016205.1:WP_011883154.1 435 SGEMDLAIAIRTGLIHNGNLYVQAAAGVVADSVPESEWQETENKARAVLRAA 486
                                               *************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (497 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: 10.85
//
[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