Alignments for a candidate for cysK in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Hydrogenovibrio marinus DSM 11271

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 WP_029909155.1 P166_RS0104435 cysteine synthase CysM

Query= BRENDA::P29848
         (303 letters)



>NCBI__GCF_000711315.1:WP_029909155.1
          Length = 297

 Score =  403 bits (1035), Expect = e-117
 Identities = 198/297 (66%), Positives = 237/297 (79%), Gaps = 1/297 (0%)

Query: 1   MNTLEQTIGNTPLVKLQRL-GPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIK 59
           M TL   +GNTPL+K+QRL   +  S I  KLEGNNPAGSVKDR AL+MI +AE RGEIK
Sbjct: 1   MKTLMDVVGNTPLIKIQRLVNANTNSVILAKLEGNNPAGSVKDRPALNMIKQAELRGEIK 60

Query: 60  PGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGM 119
           PGD LIEATSGNTGIALAM+AA+ GY+MKL+MPDNMS ER+A+M AYGAELILV+KE+GM
Sbjct: 61  PGDTLIEATSGNTGIALAMVAAMLGYKMKLIMPDNMSMERKASMAAYGAELILVSKEEGM 120

Query: 120 EGARDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTI 179
           EGARDLA  M   G+G +LDQF NPDNP AHY TTGPEIW +T G ITHFVS+MGTTGTI
Sbjct: 121 EGARDLAQKMQSEGQGTVLDQFANPDNPLAHYFTTGPEIWDETEGNITHFVSAMGTTGTI 180

Query: 180 TGVSRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAEN 239
            G S +L+EQ   + +VG+QP EGSSIPGIRRWP EY+P I++ S VD  +D+ Q  AE+
Sbjct: 181 MGTSMYLKEQNPDIQVVGVQPTEGSSIPGIRRWPKEYLPSIYDDSRVDRTIDMSQALAED 240

Query: 240 TMRELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVFGEEH 296
           TM+ +A  EGIF GVSSGGA+A AL++A  T  A++V I+CDRGDRYLSTGVF  ++
Sbjct: 241 TMKRMAKEEGIFAGVSSGGAMAAALQIANETENALIVTIVCDRGDRYLSTGVFNPKN 297


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: 366
Number of extensions: 12
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: 303
Length of database: 297
Length adjustment: 27
Effective length of query: 276
Effective length of database: 270
Effective search space:    74520
Effective search space used:    74520
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 WP_029909155.1 P166_RS0104435 (cysteine synthase CysM)
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.2258570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-154  498.7   0.9   3.3e-154  498.6   0.9    1.0  1  NCBI__GCF_000711315.1:WP_029909155.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711315.1:WP_029909155.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.6   0.9  3.3e-154  3.3e-154       1     290 []       3     293 ..       3     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 498.6 bits;  conditional E-value: 3.3e-154
                             TIGR01138   1 tilklvGntplvrlkrllpe.edsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGi 72 
                                           t++++vGntpl++++rl    ++s +l+klegnnpaGsvkdrpal mi +ae+rGeik+Gd+lieatsGntGi
  NCBI__GCF_000711315.1:WP_029909155.1   3 TLMDVVGNTPLIKIQRLVNAnTNSVILAKLEGNNPAGSVKDRPALNMIKQAELRGEIKPGDTLIEATSGNTGI 75 
                                           799*************98763778899********************************************** PP

                             TIGR01138  73 alamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnp 145
                                           alamvaa++Gyk+kl+mpdn+s erka + ayGaelilv+keeGmeGardla++++ +g++ +ldqf+npdnp
  NCBI__GCF_000711315.1:WP_029909155.1  76 ALAMVAAMLGYKMKLIMPDNMSMERKASMAAYGAELILVSKEEGMEGARDLAQKMQSEGQGTVLDQFANPDNP 148
                                           ************************************************************************* PP

                             TIGR01138 146 kahytstGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgi 218
                                            ahy++tG+eiw++t+G+ithfvs++GttGtimG+s +lkeqnp++q+vG+qp+egs+i+G+rr+++eylp i
  NCBI__GCF_000711315.1:WP_029909155.1 149 LAHYFTTGPEIWDETEGNITHFVSAMGTTGTIMGTSMYLKEQNPDIQVVGVQPTEGSSIPGIRRWPKEYLPSI 221
                                           ************************************************************************* PP

                             TIGR01138 219 fdaslvdrvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290
                                           +d+s+vdr++d+ q  aed+++++ak+egif GvssGga+aaal++a+e e+a++v+i+cdrGdrylstgvf
  NCBI__GCF_000711315.1:WP_029909155.1 222 YDDSRVDRTIDMSQALAEDTMKRMAKEEGIFAGVSSGGAMAAALQIANETENALIVTIVCDRGDRYLSTGVF 293
                                           ***********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (297 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: 23.90
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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