Alignments for a candidate for cysK in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Shewanella oneidensis MR-1

Align S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 202695 SO3598 cysteine synthase B (NCBI ptt file)

Query= BRENDA::P29848
         (303 letters)



>FitnessBrowser__MR1:202695
          Length = 288

 Score =  378 bits (971), Expect = e-110
 Identities = 195/291 (67%), Positives = 234/291 (80%), Gaps = 6/291 (2%)

Query: 3   TLEQTIGNTPLVKLQRLGPDNGSE-IWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPG 61
           T+E  IG TPLV+LQRL  D GS  + +KLEGNNPAGSVKDRAAL+MI +AE R EI PG
Sbjct: 2   TIEACIGQTPLVRLQRL--DCGSSTVLLKLEGNNPAGSVKDRAALNMINQAELRQEIAPG 59

Query: 62  DVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEG 121
           D LIEATSGNTGIALAM AA+KGY+M L+MP N +QER+ AM+AYGAEL+LV     ME 
Sbjct: 60  DTLIEATSGNTGIALAMAAAIKGYKMILIMPSNSTQERKDAMQAYGAELLLV---DNMEA 116

Query: 122 ARDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTITG 181
           ARDLALA+   G+GK+LDQFNN DN  AH+ TTGPEIW+Q+ G+ITHFVSSMGTTGTI G
Sbjct: 117 ARDLALALQAEGKGKVLDQFNNQDNANAHFLTTGPEIWQQSQGKITHFVSSMGTTGTIMG 176

Query: 182 VSRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENTM 241
           VS++L+ +   +TIVGLQP +GSSIPGIRRWP EY+PGIF+A+ VD ++DI + DA+   
Sbjct: 177 VSKYLKSRNPDITIVGLQPADGSSIPGIRRWPQEYLPGIFDAARVDLMMDIEEQDAKAMA 236

Query: 242 RELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVF 292
           R LA  EGI  GVSSGGAV  AL +AR  PG++VVAI+CDRGDRYLS+G+F
Sbjct: 237 RALAREEGICAGVSSGGAVYAALELARQYPGSVVVAIVCDRGDRYLSSGLF 287


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: 328
Number of extensions: 12
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: 288
Length adjustment: 26
Effective length of query: 277
Effective length of database: 262
Effective search space:    72574
Effective search space used:    72574
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 202695 SO3598 (cysteine synthase B (NCBI ptt file))
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.23382.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.3e-142  458.5   0.1     6e-142  458.3   0.1    1.0  1  lcl|FitnessBrowser__MR1:202695  SO3598 cysteine synthase B (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202695  SO3598 cysteine synthase B (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.3   0.1    6e-142    6e-142       1     290 []       2     287 ..       2     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 458.3 bits;  conditional E-value: 6e-142
                       TIGR01138   1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGialamvaa 79 
                                     ti+ ++G tplvrl+rl    +s+vl+klegnnpaGsvkdr+al mi +ae+r ei +Gd+lieatsGntGialam+aa
  lcl|FitnessBrowser__MR1:202695   2 TIEACIGQTPLVRLQRLDCG-SSTVLLKLEGNNPAGSVKDRAALNMINQAELRQEIAPGDTLIEATSGNTGIALAMAAA 79 
                                     89**************9875.789******************************************************* PP

                       TIGR01138  80 lkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahytstGieiwq 158
                                     +kGyk++l+mp+n+++erk a++ayGael+lvd+   me ardla  l+ +g++k+ldqfnn dn +ah+ +tG+eiwq
  lcl|FitnessBrowser__MR1:202695  80 IKGYKMILIMPSNSTQERKDAMQAYGAELLLVDN---MEAARDLALALQAEGKGKVLDQFNNQDNANAHFLTTGPEIWQ 155
                                     ********************************86...899*************************************** PP

                       TIGR01138 159 qtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslvdrvvdveqedaed 237
                                     q++G+ithfvss+GttGtimGvs++lk +np+++ivGlqpa+gs+i+G+rr+++eylpgifda++vd ++d+e++da+ 
  lcl|FitnessBrowser__MR1:202695 156 QSQGKITHFVSSMGTTGTIMGVSKYLKSRNPDITIVGLQPADGSSIPGIRRWPQEYLPGIFDAARVDLMMDIEEQDAKA 234
                                     ******************************************************************************* PP

                       TIGR01138 238 iarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290
                                     +ar la++egi  GvssGgav+aal+lar+ + +vvvai+cdrGdryls+g+f
  lcl|FitnessBrowser__MR1:202695 235 MARALAREEGICAGVSSGGAVYAALELARQYPGSVVVAIVCDRGDRYLSSGLF 287
                                     ***************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (288 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.88
//
[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