Alignments for a candidate for cysK in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_0220 Echvi_0220 cysteine synthase B

Query= BRENDA::P29848
         (303 letters)



>FitnessBrowser__Cola:Echvi_0220
          Length = 292

 Score =  315 bits (807), Expect = 8e-91
 Identities = 159/290 (54%), Positives = 210/290 (72%)

Query: 4   LEQTIGNTPLVKLQRLGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDV 63
           L + IGNTPLV+L+ +  +   +I+ KLEG NP GSVKDRAA SMI  A  RG++K GD 
Sbjct: 3   LFELIGNTPLVELEHIPTNPNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRGDLKQGDR 62

Query: 64  LIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGAR 123
           ++EATSGNTGIALAMIA + G  M L+MPDN ++ER  +M AYGA++IL    + +E +R
Sbjct: 63  VVEATSGNTGIALAMIAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAAKTIEYSR 122

Query: 124 DLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTITGVS 183
            LA  M++     +L+QF NPDN  AHY  TGPEI R T+G ITHFVS+MGTTGTI GVS
Sbjct: 123 TLAEEMAKNEGYYILNQFANPDNYQAHYEGTGPEIMRDTNGEITHFVSAMGTTGTIMGVS 182

Query: 184 RFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENTMRE 243
           R+L+EQ+  V IVG QP +GSSIPGIRRW  E++P I++AS VD+++D+ Q +A    R 
Sbjct: 183 RYLKEQKPAVQIVGTQPTDGSSIPGIRRWSPEFLPKIYDASRVDQIIDVSQEEATEMTRR 242

Query: 244 LAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVFG 293
           +A  EGI  G+SSGGA+  A+++A +    ++V I CDRGDRYLS+ +FG
Sbjct: 243 MAKEEGILAGMSSGGALHAAVKLAESLDSGVIVCITCDRGDRYLSSDLFG 292


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: 306
Number of extensions: 11
Number of successful extensions: 1
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 Echvi_0220 Echvi_0220 (cysteine synthase B)
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.25715.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.2e-129  415.9   0.1   5.8e-129  415.7   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0220  Echvi_0220 cysteine synthase B


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0220  Echvi_0220 cysteine synthase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7   0.1  5.8e-129  5.8e-129       3     290 .]       4     291 ..       2     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 5.8e-129
                            TIGR01138   3 lklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGialam 76 
                                           +l+Gntplv l++++++ +++++ kleg+np+Gsvkdr+a smi +a  rG++k+Gd ++eatsGntGialam
  lcl|FitnessBrowser__Cola:Echvi_0220   4 FELIGNTPLVELEHIPTNPNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRGDLKQGDRVVEATSGNTGIALAM 77 
                                          689*********************************************************************** PP

                            TIGR01138  77 vaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahyt 150
                                          +a ++G++++l+mpdn+++er   ++ayGa++il+   + +e +r la+e++++    +l+qf+npdn++ahy 
  lcl|FitnessBrowser__Cola:Echvi_0220  78 IAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAAKTIEYSRTLAEEMAKNEGYYILNQFANPDNYQAHYE 151
                                          ****************************************************999999**************** PP

                            TIGR01138 151 stGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslv 224
                                           tG+ei + t+G ithfvs++GttGtimGvsr+lkeq+pavqivG qp++gs+i+G+rr+  e+lp+i+das+v
  lcl|FitnessBrowser__Cola:Echvi_0220 152 GTGPEIMRDTNGEITHFVSAMGTTGTIMGVSRYLKEQKPAVQIVGTQPTDGSSIPGIRRWSPEFLPKIYDASRV 225
                                          ************************************************************************** PP

                            TIGR01138 225 drvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290
                                          d+++dv qe+a ++ r++ak+egi+ G+ssGga+ aa++la  l+ +v+v+i cdrGdryls+ +f
  lcl|FitnessBrowser__Cola:Echvi_0220 226 DQIIDVSQEEATEMTRRMAKEEGILAGMSSGGALHAAVKLAESLDSGVIVCITCDRGDRYLSSDLF 291
                                          ***************************************************************987 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.00
//
[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