Alignments for a candidate for trpE in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Shewanella amazonensis SB2B

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate 6937996 Sama_2129 anthranilate synthase component I (RefSeq)

Query= SwissProt::P00898
         (520 letters)



>FitnessBrowser__SB2B:6937996
          Length = 527

 Score =  503 bits (1294), Expect = e-147
 Identities = 275/502 (54%), Positives = 348/502 (69%), Gaps = 14/502 (2%)

Query: 17  YRENPTALFHQVCGDRPATLLLESADIDSKDDLKSLLLVDSALRITALGDTVTIQALSDN 76
           Y+++P AL+  +  D   TLLLESA+IDSK++LKS+++  +AL+I A G  +   AL DN
Sbjct: 26  YQDDPLALYESLTQDAHHTLLLESAEIDSKENLKSIIMTHAALKIAAQGYRLEFTALDDN 85

Query: 77  GASLLPLLDTALPAGVENDVLPAGRVLRFPPV--SPLLDEDARLCSLSVFDAFRLLQGVV 134
           G  LLP +     AG  N  L     L       + LLDEDARL S S  D  R L   +
Sbjct: 86  GRVLLPAI-----AGFFNCELTETNYLAVTLTRDTGLLDEDARLKSTSPLDGLRALLKHI 140

Query: 135 NIPTQER-EAMFFGGLFAYDLVAGFEALPHLEAG-NNCPDYCFYLAETLMVIDHQKKSTR 192
           ++  +   E +F GG+ AYDL+   E LP    G N CPDY FYLA+TL+++DH+ K   
Sbjct: 141 HVGEKVAFEDLFLGGVLAYDLIDTVEPLPKARDGANTCPDYLFYLADTLVLVDHKAKQAE 200

Query: 193 IQASLFTASDRE----KQRLNARLAYLSQQLTQPAPPLPVTPVPDMRCECNQSDDAFGAV 248
           +  S F+A  +     +  L  R   +     +P P   + PV ++    + SD+ F   
Sbjct: 201 LVLSTFSADGQISPFIEDELKRRAKVIEAIANRPRPVKALKPV-NVEASVSISDEDFKDA 259

Query: 249 VRQLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDNDFTLFGASP 308
           V  L++ I AG+IFQVVPSR FSLPCP+ L AY  L+K+NPSPYMF+ + +DFTLFGASP
Sbjct: 260 VNALKEHIIAGDIFQVVPSRSFSLPCPNTLGAYRALRKTNPSPYMFYFRSSDFTLFGASP 319

Query: 309 ESSLKYDAASRQIEIYPIAGTRPRGRRADGTLDRDLDSRIELDMRTDHKELSEHLMLVDL 368
           ES+LKYDA S Q+E+YPIAGTR RG+ A G +D DLD RIEL++R D KELSEHLMLVDL
Sbjct: 320 ESALKYDADSNQVEVYPIAGTRKRGKDASGNIDHDLDGRIELELRLDKKELSEHLMLVDL 379

Query: 369 ARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRACMNMGTLSG 428
           ARND+ARI   G+R VA+L KVDRYS+VMHLVSRV G+LR DLDALHAY+ACMNMGTL+G
Sbjct: 380 ARNDIARISQSGTRKVAELLKVDRYSHVMHLVSRVTGQLRQDLDALHAYQACMNMGTLTG 439

Query: 429 APKVRAMQLIADAEGQRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATVQAGAGIVL 488
           APKVRA QLI + E  RRGSYGGAVGY +A GD+DTCIVIRSA V++G+A +QAGAG+V 
Sbjct: 440 APKVRASQLIRETEKTRRGSYGGAVGYLSATGDMDTCIVIRSAFVKDGLAHIQAGAGVVY 499

Query: 489 DSVPQSEADETRNKARAVLRAI 510
           DS PQ+EADETR KA+AV+ AI
Sbjct: 500 DSDPQAEADETRQKAQAVISAI 521


Lambda     K      H
   0.321    0.136    0.396 

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: 634
Number of extensions: 18
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: 520
Length of database: 527
Length adjustment: 35
Effective length of query: 485
Effective length of database: 492
Effective search space:   238620
Effective search space used:   238620
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 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 6937996 Sama_2129 (anthranilate synthase component I (RefSeq))
to HMM TIGR00565 (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/TIGR00565.hmm
# target sequence database:        /tmp/gapView.2178.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00565  [M=498]
Accession:   TIGR00565
Description: trpE_proteo: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-214  699.3   0.1     2e-214  699.0   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6937996  Sama_2129 anthranilate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937996  Sama_2129 anthranilate synthase component I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.0   0.1    2e-214    2e-214       1     494 [.      26     522 ..      26     524 .. 0.94

  Alignments for each domain:
  == domain 1  score: 699.0 bits;  conditional E-value: 2e-214
                         TIGR00565   1 yiadptalfeklcqdrpatlllesaeieskddlkslllvdaalkitclgdivtikalsnnGeallkkldaalkalve 77 
                                       y++dp+al+e l+qd  +tlllesaei+sk++lks+++ +aalki ++g  + ++al +nG+ ll  +  ++++   
  lcl|FitnessBrowser__SB2B:6937996  26 YQDDPLALYESLTQDAHHTLLLESAEIDSKENLKSIIMTHAALKIAAQGYRLEFTALDDNGRVLLPAIAGFFNCE-- 100
                                       89***********************************************************************99.. PP

                         TIGR00565  78 avqsenalvlrflkvkklldedakllsasvfdalr.llkslkqkpkep.ealllgGlfsydlvanfedlpqlkaknd 152
                                         ++ n l ++ ++   lldeda+l s+s++d+lr llk ++   k   e l+lgG+++ydl+ + e+lp+ +   +
  lcl|FitnessBrowser__SB2B:6937996 101 -LTETNYLAVTLTRDTGLLDEDARLKSTSPLDGLRaLLKHIHVGEKVAfEDLFLGGVLAYDLIDTVEPLPKARDGAN 176
                                       .678899****************************99****9999998789************************** PP

                         TIGR00565 153 nvpdfifylaenlividhkeksveikaalfaereekqvaiakldlkeaqk.....skkadfvpkvsaasreveanls 224
                                       ++pd+ fyla++l+++dhk k++e+  + f+ + +    i+  +lk+ +k     +++  +v   +  + e ++ +s
  lcl|FitnessBrowser__SB2B:6937996 177 TCPDYLFYLADTLVLVDHKAKQAELVLSTFSADGQISPFIED-ELKRRAKvieaiANRPRPVKALKPVNVEASVSIS 252
                                       ******************************985433333332.233333300000333445666777778888899* PP

                         TIGR00565 225 deefegvvkalkkeikkGeifqvvpsrrfslecpetlaayyqlkksnPsPymfylkdedfilfGasPesalkydaes 301
                                       de+f++ v+alk++i +G+ifqvvpsr+fsl+cp+tl ay  l+k+nPsPymfy++ +df+lfGasPesalkyda s
  lcl|FitnessBrowser__SB2B:6937996 253 DEDFKDAVNALKEHIIAGDIFQVVPSRSFSLPCPNTLGAYRALRKTNPSPYMFYFRSSDFTLFGASPESALKYDADS 329
                                       ***************************************************************************** PP

                         TIGR00565 302 rqleiyPiaGtrprGkdadGnidrdldsrlelelrldhkeraehlmlvdlarndlarvcksgkryvaellkvdrysn 378
                                       +q+e+yPiaGtr rGkda Gnid+dld r+elelrld ke++ehlmlvdlarnd+ar+++sg+r+vaellkvdrys+
  lcl|FitnessBrowser__SB2B:6937996 330 NQVEVYPIAGTRKRGKDASGNIDHDLDGRIELELRLDKKELSEHLMLVDLARNDIARISQSGTRKVAELLKVDRYSH 406
                                       ***************************************************************************** PP

                         TIGR00565 379 vmhlvsrvvGelrkeldalhayracmnmGtlsGaPkikalqliyqlenqrrgsyGGavGyltseGdldtcivirsal 455
                                       vmhlvsrv G+lr++ldalhay+acmnmGtl+GaPk++a qli + e+ rrgsyGGavGyl++ Gd+dtcivirsa+
  lcl|FitnessBrowser__SB2B:6937996 407 VMHLVSRVTGQLRQDLDALHAYQACMNMGTLTGAPKVRASQLIRETEKTRRGSYGGAVGYLSATGDMDTCIVIRSAF 483
                                       ***************************************************************************** PP

                         TIGR00565 456 vkngiavvqaGaGvvldsvPqseadetrakaravlkair 494
                                       vk+g+a++qaGaGvv ds+Pq+eadetr+ka+av+ ai+
  lcl|FitnessBrowser__SB2B:6937996 484 VKDGLAHIQAGAGVVYDSDPQAEADETRQKAQAVISAIK 522
                                       *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (498 nodes)
Target sequences:                          1  (527 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: 12.88
//
[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