Alignments for a candidate for cysK in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Pseudomonas simiae WCS417

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 GFF3937 PS417_20160 cysteine synthase

Query= SwissProt::P16703
         (303 letters)



>FitnessBrowser__WCS417:GFF3937
          Length = 300

 Score =  416 bits (1068), Expect = e-121
 Identities = 208/292 (71%), Positives = 241/292 (82%)

Query: 3   TLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGD 62
           T+   +GNTPLV+LQRM  D  + + LKLEGNNPAGSVKDR ALSMI  AE RG+IKPGD
Sbjct: 7   TIADCVGNTPLVRLQRMAGDTSNTLLLKLEGNNPAGSVKDRPALSMITRAELRGQIKPGD 66

Query: 63  VLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGA 122
            LIEATSGNTGIALAM AA+KGY+M L+MPDN S ER+AAM AYGA+LILVT+E GMEGA
Sbjct: 67  TLIEATSGNTGIALAMAAAIKGYKMILIMPDNGSAERKAAMTAYGAQLILVTQEDGMEGA 126

Query: 123 RDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGV 182
           RDLA  MA  G G +LDQF N DNP AHYT+TGPEIW+QT G ITHFVSSMGTTGTI G 
Sbjct: 127 RDLAERMAAEGRGLVLDQFANGDNPEAHYTSTGPEIWRQTQGTITHFVSSMGTTGTIMGN 186

Query: 183 SRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMR 242
           SR+++EQ+  + IVGLQP EGS+IPGIRRWP EYLP I+N+S VD ++D+ QR+AE+T R
Sbjct: 187 SRYLKEQNPAIQIVGLQPMEGSAIPGIRRWPEEYLPKIYNSSRVDRIIDMAQREAEDTTR 246

Query: 243 ELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGE 294
            LA  EGIFCGVSSGGAVAG LR++K   +AV+VAIICDRGDRYLSTG+F E
Sbjct: 247 RLAREEGIFCGVSSGGAVAGMLRLSKEVENAVIVAIICDRGDRYLSTGIFDE 298


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: 371
Number of extensions: 12
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: 300
Length adjustment: 27
Effective length of query: 276
Effective length of database: 273
Effective search space:    75348
Effective search space used:    75348
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 GFF3937 PS417_20160 (cysteine synthase)
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.18236.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-165  534.9   0.4   3.2e-165  534.7   0.4    1.0  1  lcl|FitnessBrowser__WCS417:GFF3937  PS417_20160 cysteine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3937  PS417_20160 cysteine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.7   0.4  3.2e-165  3.2e-165       1     290 []       7     296 ..       7     296 .. 1.00

  Alignments for each domain:
  == domain 1  score: 534.7 bits;  conditional E-value: 3.2e-165
                           TIGR01138   1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntGiala 75 
                                         ti+++vGntplvrl+r+++++++++l+klegnnpaGsvkdrpalsmi++ae+rG+ik+Gd+lieatsGntGiala
  lcl|FitnessBrowser__WCS417:GFF3937   7 TIADCVGNTPLVRLQRMAGDTSNTLLLKLEGNNPAGSVKDRPALSMITRAELRGQIKPGDTLIEATSGNTGIALA 81 
                                         89************************************************************************* PP

                           TIGR01138  76 mvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnpdnpkahyt 150
                                         m+aa+kGyk++l+mpdn s+erkaa++ayGa+lilv++e+GmeGardla++++ +g++ +ldqf+n+dnp+ahyt
  lcl|FitnessBrowser__WCS417:GFF3937  82 MAAAIKGYKMILIMPDNGSAERKAAMTAYGAQLILVTQEDGMEGARDLAERMAAEGRGLVLDQFANGDNPEAHYT 156
                                         *************************************************************************** PP

                           TIGR01138 151 stGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrrieseylpgifdaslvd 225
                                         stG+eiw+qt+G ithfvss+GttGtimG sr+lkeqnpa+qivGlqp+egsai+G+rr+++eylp+i+++s+vd
  lcl|FitnessBrowser__WCS417:GFF3937 157 STGPEIWRQTQGTITHFVSSMGTTGTIMGNSRYLKEQNPAIQIVGLQPMEGSAIPGIRRWPEEYLPKIYNSSRVD 231
                                         *************************************************************************** PP

                           TIGR01138 226 rvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290
                                         r++d+ q++aed+ r+la++egif+GvssGgava++lrl++e+e+av+vaiicdrGdrylstg+f
  lcl|FitnessBrowser__WCS417:GFF3937 232 RIIDMAQREAEDTTRRLAREEGIFCGVSSGGAVAGMLRLSKEVENAVIVAIICDRGDRYLSTGIF 296
                                         ***************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (300 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: 7.00
//
[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