Alignments for a candidate for cysK in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Shewanella sp. ANA-3

Align Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 (characterized)
to candidate 7026046 Shewana3_3188 cysteine synthase B (RefSeq)

Query= SwissProt::P16703
         (303 letters)



>FitnessBrowser__ANA3:7026046
          Length = 292

 Score =  384 bits (986), Expect = e-111
 Identities = 197/291 (67%), Positives = 238/291 (81%), Gaps = 6/291 (2%)

Query: 3   TLEQTIGNTPLVKLQRMGPDNGSE-VWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPG 61
           T+E  IG TPLV+LQR+  D GS  V LKLEGNNPAGSVKDRAAL+MI++AE R EI PG
Sbjct: 6   TIEACIGQTPLVRLQRL--DCGSSTVLLKLEGNNPAGSVKDRAALNMIIQAELRQEIAPG 63

Query: 62  DVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEG 121
           D LIEATSGNTGIALAM AA+KGY+M L+MP N +QER+ AM+AYGAEL+LV     ME 
Sbjct: 64  DTLIEATSGNTGIALAMAAAIKGYKMILIMPSNSTQERKDAMQAYGAELLLV---DNMEA 120

Query: 122 ARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITG 181
           ARDLAL++  +G+GK+LDQFNN DN  AH+ TTGPEIWQQ+ G+ITHFVSSMGTTGTI G
Sbjct: 121 ARDLALDLQAQGKGKVLDQFNNQDNANAHFQTTGPEIWQQSQGKITHFVSSMGTTGTIMG 180

Query: 182 VSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTM 241
           VS++++ ++  +TIVGLQP +GSSIPGIRRWP EYLPGIF+A+ VD V+DI ++DA+   
Sbjct: 181 VSKYLKSRNPDITIVGLQPADGSSIPGIRRWPQEYLPGIFDAARVDAVMDIEEQDAKAMA 240

Query: 242 RELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVF 292
           R LA  EGI  GVSSGGAV  AL +A+ NP +VVVAI+CDRGDRYLS+G+F
Sbjct: 241 RTLAREEGICAGVSSGGAVFAALEIARQNPGSVVVAIVCDRGDRYLSSGLF 291


Lambda     K      H
   0.316    0.134    0.386 

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: 326
Number of extensions: 11
Number of successful extensions: 3
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: 303
Length of database: 292
Length adjustment: 26
Effective length of query: 277
Effective length of database: 266
Effective search space:    73682
Effective search space used:    73682
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate 7026046 Shewana3_3188 (cysteine synthase B (RefSeq))
to HMM TIGR01138 (cysM: cysteine synthase B (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/TIGR01138.hmm
# target sequence database:        /tmp/gapView.12831.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01138  [M=290]
Accession:   TIGR01138
Description: cysM: cysteine synthase B
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     5e-144  465.2   0.2   5.6e-144  465.0   0.2    1.0  1  lcl|FitnessBrowser__ANA3:7026046  Shewana3_3188 cysteine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026046  Shewana3_3188 cysteine synthase B (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.0   0.2  5.6e-144  5.6e-144       1     290 []       6     291 ..       6     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.0 bits;  conditional E-value: 5.6e-144
                         TIGR01138   1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGialamv 77 
                                       ti+ ++G tplvrl+rl    +s+vl+klegnnpaGsvkdr+al mi++ae+r ei +Gd+lieatsGntGialam+
  lcl|FitnessBrowser__ANA3:7026046   6 TIEACIGQTPLVRLQRLDCG-SSTVLLKLEGNNPAGSVKDRAALNMIIQAELRQEIAPGDTLIEATSGNTGIALAMA 81 
                                       89**************9875.789***************************************************** PP

                         TIGR01138  78 aalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahytstGi 154
                                       aa+kGyk++l+mp+n+++erk a++ayGael+lvd+   me ardla +l+ +g++k+ldqfnn dn +ah+++tG+
  lcl|FitnessBrowser__ANA3:7026046  82 AAIKGYKMILIMPSNSTQERKDAMQAYGAELLLVDN---MEAARDLALDLQAQGKGKVLDQFNNQDNANAHFQTTGP 155
                                       **********************************86...899*********************************** PP

                         TIGR01138 155 eiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslvdrvvdve 231
                                       eiwqq++G+ithfvss+GttGtimGvs++lk +np+++ivGlqpa+gs+i+G+rr+++eylpgifda++vd v+d+e
  lcl|FitnessBrowser__ANA3:7026046 156 EIWQQSQGKITHFVSSMGTTGTIMGVSKYLKSRNPDITIVGLQPADGSSIPGIRRWPQEYLPGIFDAARVDAVMDIE 232
                                       ***************************************************************************** PP

                         TIGR01138 232 qedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290
                                       ++da+ +ar la++egi  GvssGgav+aal++ar+++ +vvvai+cdrGdryls+g+f
  lcl|FitnessBrowser__ANA3:7026046 233 EQDAKAMARTLAREEGICAGVSSGGAVFAALEIARQNPGSVVVAIVCDRGDRYLSSGLF 291
                                       *********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (292 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: 7.13
//
[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