Alignments for a candidate for trpE in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpE in Shewanella loihica PV-4

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate 5209798 Shew_2251 anthranilate synthase component I (RefSeq)

Query= SwissProt::P00895
         (520 letters)



>FitnessBrowser__PV4:5209798
          Length = 517

 Score =  501 bits (1291), Expect = e-146
 Identities = 281/511 (54%), Positives = 352/511 (68%), Gaps = 34/511 (6%)

Query: 17  YRDNPTALFHQLCGDRPATLLLESADIDSKDDLKSLLLVDSALRITALGDTVTIQALSGN 76
           Y D+P  L+  L  D   T+LLESA+IDSKD LKS+++  +AL I   G  ++  ALS N
Sbjct: 18  YHDDPLQLYQHLTQDAAHTMLLESAEIDSKDHLKSIIMTHAALAIRCEGYQLSFTALSDN 77

Query: 77  GEALLA-----------LLDN-ALPAGVESEQSPNCRVLRFPPVSPLLDEDARLCSLSVF 124
           G+ALL            L+D  AL  G++ + S             LLDEDARL S S  
Sbjct: 78  GQALLVPIACFFGEDENLVDGKALTLGLQKDTS-------------LLDEDARLKSTSPL 124

Query: 125 DAFRLLQNLLNVPKEER-EAMFFGGLFSYDLVAGFEDLPQLS-AENNCPDFCFYLAETLM 182
           D  R L   +++  + + E++F GG+ ++DL+   E LP++S + N CPD+ FYLAETL+
Sbjct: 125 DGLRSLIKHIDMGDDAQFESLFLGGVLAFDLIDTVEPLPKVSQSANTCPDYLFYLAETLI 184

Query: 183 VIDHQKKSTRIQASLFAPNEEEKQRLTARLNELRQ---QLTEAAPPLPVVSVPHMRCECN 239
           ++DHQ +S  I +  F    E K  L  R+ +L Q    L + AP  PV +      + N
Sbjct: 185 LVDHQARSADIISHNFTQQAEVKAALAERVTQLHQACSSLPDIAPLCPVDA----ETQVN 240

Query: 240 QSDEEFGGVVRLLQKAIRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYMFFMQDN 299
            SD+EF  +V  L+  I AG+IFQVVPSR FSLPCP+ L AY  L+ +NPSPYMF+ + +
Sbjct: 241 VSDDEFKNIVTDLKSHIVAGDIFQVVPSRSFSLPCPNALGAYRALRLTNPSPYMFYFRGD 300

Query: 300 DFTLFGASPESSLKYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKEL 359
           DFTLFGASPES+LKY+A++ Q+EIYPIAGTR RG+ A G +D DLDSRIELE+R D KEL
Sbjct: 301 DFTLFGASPESALKYEASTNQVEIYPIAGTRKRGKTASGEIDFDLDSRIELELRLDKKEL 360

Query: 360 SEHLMLVDLARNDLARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRA 419
           SEHLMLVDLARND+ARI   G+R VA+L KVDRYS+VMHLVSRV G+LR DLDALHAY+A
Sbjct: 361 SEHLMLVDLARNDVARISQSGTRKVAELLKVDRYSHVMHLVSRVTGQLRSDLDALHAYQA 420

Query: 420 CMNMGTLSGAPKVRAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIAT 479
           CMNMGTL+GAPKV A QLI  AE  RRGSYGGAVGY    GD+DTCIVIRSA V+ G A 
Sbjct: 421 CMNMGTLTGAPKVSAAQLIRGAEKTRRGSYGGAVGYLNGLGDMDTCIVIRSAFVKEGTAH 480

Query: 480 VQAGAGVVLDSVPQSEADETRNKARAVLRAI 510
           +QAGAGVV DS PQ+EADETR KA+AV+ AI
Sbjct: 481 IQAGAGVVYDSDPQAEADETRQKAQAVISAI 511


Lambda     K      H
   0.320    0.135    0.391 

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: 618
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: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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 5209798 Shew_2251 (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.14374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.4e-215  702.8   0.1   1.6e-215  702.6   0.1    1.0  1  lcl|FitnessBrowser__PV4:5209798  Shew_2251 anthranilate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209798  Shew_2251 anthranilate synthase component I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  702.6   0.1  1.6e-215  1.6e-215       1     494 [.      18     512 ..      18     515 .. 0.97

  Alignments for each domain:
  == domain 1  score: 702.6 bits;  conditional E-value: 1.6e-215
                        TIGR00565   1 yiadptalfeklcqdrpatlllesaeieskddlkslllvdaalkitclgdivtikalsnnGeallkkldaalkalvea 78 
                                      y++dp+ l+++l+qd ++t+llesaei+skd+lks+++ +aal i c g +++++als+nG+all  +  ++    e 
  lcl|FitnessBrowser__PV4:5209798  18 YHDDPLQLYQHLTQDAAHTMLLESAEIDSKDHLKSIIMTHAALAIRCEGYQLSFTALSDNGQALLVPIACFFGED-EN 94 
                                      899*********************************************************************998.88 PP

                        TIGR00565  79 vqsenalvlrflkvkklldedakllsasvfdalr.llkslkqkpkep.ealllgGlfsydlvanfedlpqlkakndnv 154
                                          +al+l  +k   lldeda+l s+s++d+lr l+k +      + e+l+lgG++++dl+ + e+lp+++   +++
  lcl|FitnessBrowser__PV4:5209798  95 LVDGKALTLGLQKDTSLLDEDARLKSTSPLDGLRsLIKHIDMGDDAQfESLFLGGVLAFDLIDTVEPLPKVSQSANTC 172
                                      889999****************************99**999888877789**************************** PP

                        TIGR00565 155 pdfifylaenlividhkeksveikaalfaereekqvaiakldlkeaqkskkadfvpkvsaasreveanlsdeefegvv 232
                                      pd+ fylae+li++dh+ +s++i +  f ++ e + a a +  +  q   + + +      + e ++n+sd+ef+++v
  lcl|FitnessBrowser__PV4:5209798 173 PDYLFYLAETLILVDHQARSADIISHNFTQQAEVKAALAERVTQLHQACSSLPDIAPLCPVDAETQVNVSDDEFKNIV 250
                                      ******************************9887777777666667777777777777888999************** PP

                        TIGR00565 233 kalkkeikkGeifqvvpsrrfslecpetlaayyqlkksnPsPymfylkdedfilfGasPesalkydaesrqleiyPia 310
                                        lk +i +G+ifqvvpsr+fsl+cp++l ay  l+ +nPsPymfy++ +df+lfGasPesalky+a ++q+eiyPia
  lcl|FitnessBrowser__PV4:5209798 251 TDLKSHIVAGDIFQVVPSRSFSLPCPNALGAYRALRLTNPSPYMFYFRGDDFTLFGASPESALKYEASTNQVEIYPIA 328
                                      ****************************************************************************** PP

                        TIGR00565 311 GtrprGkdadGnidrdldsrlelelrldhkeraehlmlvdlarndlarvcksgkryvaellkvdrysnvmhlvsrvvG 388
                                      Gtr rGk a G+id dldsr+elelrld ke++ehlmlvdlarnd+ar+++sg+r+vaellkvdrys+vmhlvsrv G
  lcl|FitnessBrowser__PV4:5209798 329 GTRKRGKTASGEIDFDLDSRIELELRLDKKELSEHLMLVDLARNDVARISQSGTRKVAELLKVDRYSHVMHLVSRVTG 406
                                      ****************************************************************************** PP

                        TIGR00565 389 elrkeldalhayracmnmGtlsGaPkikalqliyqlenqrrgsyGGavGyltseGdldtcivirsalvkngiavvqaG 466
                                      +lr +ldalhay+acmnmGtl+GaPk++a qli  +e+ rrgsyGGavGyl+  Gd+dtcivirsa+vk+g a++qaG
  lcl|FitnessBrowser__PV4:5209798 407 QLRSDLDALHAYQACMNMGTLTGAPKVSAAQLIRGAEKTRRGSYGGAVGYLNGLGDMDTCIVIRSAFVKEGTAHIQAG 484
                                      ****************************************************************************** PP

                        TIGR00565 467 aGvvldsvPqseadetrakaravlkair 494
                                      aGvv ds+Pq+eadetr+ka+av+ ai+
  lcl|FitnessBrowser__PV4:5209798 485 AGVVYDSDPQAEADETRQKAQAVISAIK 512
                                      **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (498 nodes)
Target sequences:                          1  (517 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.87
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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