Alignments for a candidate for trpE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Paraburkholderia bryophila 376MFSha3.1

Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate H281DRAFT_05715 H281DRAFT_05715 anthranilate synthase, component I

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__Burk376:H281DRAFT_05715
          Length = 497

 Score =  536 bits (1380), Expect = e-157
 Identities = 277/500 (55%), Positives = 358/500 (71%), Gaps = 14/500 (2%)

Query: 1   MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLA----DAPNSYLLESVQGGEKWG 56
           M   EF  LA +G+NRIPL  E LAD +TPLS+YLKLA    +  NS+LLESV GGE++G
Sbjct: 1   MTELEFQSLANEGFNRIPLIAEALADLETPLSLYLKLAQPERNGANSFLLESVVGGERFG 60

Query: 57  RYSIIGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFD 116
           RYS IGLP RT+LR  +    +  DG   E  +  DPL F+++F++R++V   PGLPRF 
Sbjct: 61  RYSFIGLPARTLLRTRNGVSEVVRDGKVVETHE-GDPLEFIQQFQSRFKVAQRPGLPRFA 119

Query: 117 GGLVGYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPS 176
           GGL GYFGYD VRY+EK+LA     D L  PDI L++++ V V DNLAGK++ ++ ADP+
Sbjct: 120 GGLAGYFGYDAVRYIEKKLAHSAPKDDLNLPDIQLLLTEEVAVIDNLAGKLYLVIYADPT 179

Query: 177 EENAYERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDY 236
           +  AY + + RL EL +RLR  + P     + +A  R   +R  F ++DY  AV + K+Y
Sbjct: 180 QPEAYTKAKQRLRELRQRLRATVEP----PVTSASVRTETYR-EFAKDDYLAAVRKAKEY 234

Query: 237 ILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRV 296
           I AG+ MQV   QR++  ++  P+ LYRALR  NP+PYMY++NFGDFHVVG+SPE+LVR 
Sbjct: 235 IAAGELMQVQVGQRLTKPYRDNPLSLYRALRSLNPSPYMYYYNFGDFHVVGASPEILVRQ 294

Query: 297 E----DGLVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSD 352
           E    D +VT+RP+AGTRPRG   E D  L  +LL+D KEIAEH+MLIDL RNDVGR++ 
Sbjct: 295 EKRGEDRIVTIRPLAGTRPRGNTPERDAELATELLNDPKEIAEHVMLIDLARNDVGRIAQ 354

Query: 353 IGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEII 412
           IG+V VT+KMVIE+YS+V HIVS+V G+L+ G +  D LRA  PAGTLSGAPK+RAME+I
Sbjct: 355 IGSVVVTDKMVIEKYSHVQHIVSSVEGKLKPGTTNFDVLRATFPAGTLSGAPKVRAMELI 414

Query: 413 DELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEE 472
           DELEPVKRG+YGGAVGYL++ G MD AI IRT VI NG L+VQA  G+VADSVP  EW+E
Sbjct: 415 DELEPVKRGLYGGAVGYLSFTGEMDLAITIRTGVIANGNLYVQAAAGVVADSVPESEWQE 474

Query: 473 TINKRRAMFRAVALAEQSVE 492
           T NK RA+ RA    +  ++
Sbjct: 475 TENKARAVLRAAEQVQDGLD 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: 632
Number of extensions: 29
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: 497
Length adjustment: 34
Effective length of query: 458
Effective length of database: 463
Effective search space:   212054
Effective search space used:   212054
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 H281DRAFT_05715 H281DRAFT_05715 (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.4894.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   8.6e-170  551.5   0.0   9.9e-170  551.3   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05715  H281DRAFT_05715 anthranilate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05715  H281DRAFT_05715 anthranilate synthase, component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.3   0.0  9.9e-170  9.9e-170       1     454 [.      25     486 ..      25     487 .. 0.94

  Alignments for each domain:
  == domain 1  score: 551.3 bits;  conditional E-value: 9.9e-170
                                    TIGR00564   1 adtltpisvylklak.r...kesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeea 62 
                                                  ad +tp+s+ylkla+ +   ++sfllEsv  +e+ gRyS+igl  ++ +++++g + ++  d++  
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715  25 ADLETPLSLYLKLAQpErngANSFLLESVVGGERFGRYSFIGLPARTLLRTRNG-VSEVVRDGKVV 89 
                                                  5889**********97568899*********************99999999987.55555565555 PP

                                    TIGR00564  63 k.ieedelkelrklleka.eesedeldeplsggavGylgydtvrlveklke..eaedelelpdlll 124
                                                  + +e+d+l+ ++++ +++   ++++l+  ++gg+ Gy+gyd vr++ek+ +  +++d+l+lpd+ l
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715  90 EtHEGDPLEFIQQFQSRFkVAQRPGLPR-FAGGLAGYFGYDAVRYIEKKLAhsAPKDDLNLPDIQL 154
                                                  55899*************6667788887.******************99774345*********** PP

                                    TIGR00564 125 llvetvivfDhvekkvilienarteaersaeeeaaarleellaelqkelekavkaleekkesftsn 190
                                                  ll+e+v+v D+ + k++l+ +a  ++ + a+++a++rl+el ++l+ ++e+ v+    ++e++  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 155 LLTEEVAVIDNLAGKLYLVIYADPTQPE-AYTKAKQRLRELRQRLRATVEPPVTSASVRTETY-RE 218
                                                  **********************888777.9********************9998777777666.99 PP

                                    TIGR00564 191 vekeeyeekvakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelv 256
                                                  + k++y ++v+kakeyi+aG+++qv++ qrl+++ + +p++lYr+LR+ NPSpy+yy ++ df++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 219 FAKDDYLAAVRKAKEYIAAGELMQVQVGQRLTKPYRDNPLSLYRALRSLNPSPYMYYYNFGDFHVV 284
                                                  ****************************************************************** PP

                                    TIGR00564 257 gsSPEllvkvk...gkr.vetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDig 318
                                                  g+SPE+lv+ +   ++r v++rP+AGtr+RG+t+e D+ l++eLl+d+Ke AEH+mL+DLaRND+g
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 285 GASPEILVRQEkrgEDRiVTIRPLAGTRPRGNTPERDAELATELLNDPKEIAEHVMLIDLARNDVG 350
                                                  *********9977534479*********************************************** PP

                                    TIGR00564 319 kvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelide 384
                                                  ++a++gsv v++ + iekyshv+HivS+VeG+lk+++t++D+lra++PaGTlsGAPKvrAmelide
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 351 RIAQIGSVVVTDKMVIEKYSHVQHIVSSVEGKLKPGTTNFDVLRATFPAGTLSGAPKVRAMELIDE 416
                                                  ****************************************************************** PP

                                    TIGR00564 385 lEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakal 450
                                                  lE++kRg+YgGavgylsf g++d ai+iRt v+ +g +yvqA+aG+VaDS+pe+E++Et nKa+a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 417 LEPVKRGLYGGAVGYLSFTGEMDLAITIRTGVIANGNLYVQAAAGVVADSVPESEWQETENKARAV 482
                                                  ****************************************************************** PP

                                    TIGR00564 451 lrai 454
                                                  lra+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05715 483 LRAA 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.96
//
[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