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

GapMind for Amino acid biosynthesis

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

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 5209934 Shew_2382 cysteine synthase A (RefSeq)

Query= BRENDA::P0ABK5
         (323 letters)



>FitnessBrowser__PV4:5209934
          Length = 322

 Score =  480 bits (1235), Expect = e-140
 Identities = 242/320 (75%), Positives = 273/320 (85%), Gaps = 1/320 (0%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60
           MSKIFEDNS TIG+TPLVRLNR+  G +LAKVE+RNPSFSVKCRIGANMIWDAEK+G+L 
Sbjct: 1   MSKIFEDNSYTIGNTPLVRLNRVSKGNVLAKVEARNPSFSVKCRIGANMIWDAEKKGLLT 60

Query: 61  PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120
              EL+EPTSGNTGIALAYVAAARGYKLTLTMP TMS+ERRKLLKALGANLVLTEGAKGM
Sbjct: 61  KDKELIEPTSGNTGIALAYVAAARGYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGM 120

Query: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180
           KGAI KAEE+  S PEKYL+L QF NPANPEIHEKTTGPEIW DTDG+VDV +AGVGTGG
Sbjct: 121 KGAIDKAEELRQSAPEKYLILGQFDNPANPEIHEKTTGPEIWNDTDGEVDVVVAGVGTGG 180

Query: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240
           T+TGVSRYIK T+GK  + SVAVEP DSPVI Q +AG+ ++PGPHKIQGIGAGFIP NLD
Sbjct: 181 TITGVSRYIKQTQGKA-ITSVAVEPADSPVIGQTMAGQPVQPGPHKIQGIGAGFIPGNLD 239

Query: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300
           L ++D+V  +TNEEAI  A+RLM+EEGIL GISSGAAV AA ++ +   F  KNIVVILP
Sbjct: 240 LDVIDRVEAVTNEEAIEMAQRLMKEEGILVGISSGAAVVAANRIADLPEFEGKNIVVILP 299

Query: 301 SSGERYLSTALFADLFTEKE 320
           S+ ERYLS+ LF   F + E
Sbjct: 300 SAAERYLSSVLFQGQFGDAE 319


Lambda     K      H
   0.313    0.133    0.368 

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: 415
Number of extensions: 16
Number of successful extensions: 2
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: 323
Length of database: 322
Length adjustment: 28
Effective length of query: 295
Effective length of database: 294
Effective search space:    86730
Effective search space used:    86730
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 5209934 Shew_2382 (cysteine synthase A (RefSeq))
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

# 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/TIGR01139.hmm
# target sequence database:        /tmp/gapView.16633.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01139  [M=298]
Accession:   TIGR01139
Description: cysK: cysteine synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   9.6e-146  470.6   1.1   1.1e-145  470.5   1.1    1.0  1  lcl|FitnessBrowser__PV4:5209934  Shew_2382 cysteine synthase A (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209934  Shew_2382 cysteine synthase A (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.5   1.1  1.1e-145  1.1e-145       2     298 .]       9     311 ..       8     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 470.5 bits;  conditional E-value: 1.1e-145
                        TIGR01139   2 seliGntPlvrLnlaeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGialamvaaar 79 
                                      s +iGntPlvrLn     k++vl+k+e +nPs+svk+ri+++mi+daek+gll+k+k+++e+tsGntGiala+vaaar
  lcl|FitnessBrowser__PV4:5209934   9 SYTIGNTPLVRLN--RVSKGNVLAKVEARNPSFSVKCRIGANMIWDAEKKGLLTKDKELIEPTSGNTGIALAYVAAAR 84 
                                      679**********..44479********************************************************** PP

                        TIGR01139  80 gykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpeihrkttapeil 157
                                      gykl+ltmp+tmslerrkllka+Ga+lvLt+ga+gmkgai+kaeel ++ p+kyl+l qf+npanpeih+ktt+pei+
  lcl|FitnessBrowser__PV4:5209934  85 GYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGMKGAIDKAEELRQSAPEKYLILGQFDNPANPEIHEKTTGPEIW 162
                                      ****************************************************************************** PP

                        TIGR01139 158 kdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgphkiqGigagfiPkvLdk 228
                                      +d+dg++d++vagvGtGGtitGv++++k++++  i++vavePa+spv+ ++      +pgphkiqGigagfiP +Ld 
  lcl|FitnessBrowser__PV4:5209934 163 NDTDGEVDVVVAGVGTGGTITGVSRYIKQTQGkAITSVAVEPADSPVIGQTmagqpvQPGPHKIQGIGAGFIPGNLDL 240
                                      *****************************99979***************99999999********************* PP

                        TIGR01139 229 evidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlstaLf 298
                                      +vid+v +v++eeaie+a+rl+keeGilvGissGaav+aa ++a  +e ++k+ivvilp+++erYls  Lf
  lcl|FitnessBrowser__PV4:5209934 241 DVIDRVEAVTNEEAIEMAQRLMKEEGILVGISSGAAVVAANRIADLPEfEGKNIVVILPSAAERYLSSVLF 311
                                      ********************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (322 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: 9.13
//
[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