Alignments for a candidate for cysK in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Acidovorax sp. GW101-3H11

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 Ac3H11_644 Cysteine synthase B (EC 2.5.1.47)

Query= SwissProt::P16703
         (303 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_644
          Length = 300

 Score =  379 bits (973), Expect = e-110
 Identities = 190/294 (64%), Positives = 231/294 (78%), Gaps = 4/294 (1%)

Query: 3   TLEQTIGNTPLVKLQRMGPDN----GSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEI 58
           T+E  +GNTPLV LQR+G  +    G+ V  KLEGNNPAGSVKDR ALSMI  AE+RG+I
Sbjct: 5   TIEDAVGNTPLVALQRIGAQDNAARGNVVLGKLEGNNPAGSVKDRPALSMIRRAEERGDI 64

Query: 59  KPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQG 118
           +PGD LIEATSGNTGIALAM AA+KGYRM L+MP+++S ER   M+A+GAEL+L  K  G
Sbjct: 65  RPGDTLIEATSGNTGIALAMAAAIKGYRMVLVMPEDLSIERAQTMKAFGAELVLTPKSGG 124

Query: 119 MEGARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGT 178
           ME ARDLA  M  RGEGK+LDQF NPDNP  HY TTGPEIW+QTGGRITHFVS+MGTTGT
Sbjct: 125 MEHARDLAEAMQKRGEGKVLDQFANPDNPRIHYETTGPEIWEQTGGRITHFVSAMGTTGT 184

Query: 179 ITGVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAE 238
           ITGVSRF++E++  + I+G QPEEGS IPGIR+WP EYLP I++AS VDE++ + Q +AE
Sbjct: 185 ITGVSRFLKEKNPGIQIIGAQPEEGSRIPGIRKWPQEYLPKIYDASTVDELVYVGQDNAE 244

Query: 239 NTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVF 292
           +  R LA  EGIF G+S+ GA   A ++A    +A +V ++CDRGDRYLSTGVF
Sbjct: 245 DMCRRLAREEGIFAGISAAGACWVAQQIAARESNATIVFVVCDRGDRYLSTGVF 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: 373
Number of extensions: 15
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: 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 Ac3H11_644 (Cysteine synthase B (EC 2.5.1.47))
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.32344.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     4e-143  462.2   0.1   4.5e-143  462.0   0.1    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644  Cysteine synthase B (EC 2.5.1.47


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644  Cysteine synthase B (EC 2.5.1.47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.0   0.1  4.5e-143  4.5e-143       1     290 []       5     298 ..       5     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 462.0 bits;  conditional E-value: 4.5e-143
                                       TIGR01138   1 tilklvGntplvrlkrllpe....edsevlvklegnnpaGsvkdrpalsmiveaekrGeikeG 59 
                                                     ti+++vGntplv l+r++++     ++ vl klegnnpaGsvkdrpalsmi +ae rG+i++G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644   5 TIEDAVGNTPLVALQRIGAQdnaaRGNVVLGKLEGNNPAGSVKDRPALSMIRRAEERGDIRPG 67 
                                                     89***************998667678899********************************** PP

                                       TIGR01138  60 dvlieatsGntGialamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGard 122
                                                     d+lieatsGntGialam+aa+kGy++ l+mp++ s er + +ka+Gael+l+ k  Gme ard
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644  68 DTLIEATSGNTGIALAMAAAIKGYRMVLVMPEDLSIERAQTMKAFGAELVLTPKSGGMEHARD 130
                                                     *************************************************************** PP

                                       TIGR01138 123 larelvrkgeeklldqfnnpdnpkahytstGieiwqqtkGrithfvsslGttGtimGvsrflk 185
                                                     la+ ++++ge+k+ldqf+npdnp+ hy +tG+eiw+qt+Grithfvs++GttGti+Gvsrflk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644 131 LAEAMQKRGEGKVLDQFANPDNPRIHYETTGPEIWEQTGGRITHFVSAMGTTGTITGVSRFLK 193
                                                     *************************************************************** PP

                                       TIGR01138 186 eqnpavqivGlqpaegsaieGlrrieseylpgifdaslvdrvvdveqedaediarelakkegi 248
                                                     e+np +qi+G qp+egs i+G+r++++eylp+i+das vd+ v+v q++aed+ r+la++egi
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644 194 EKNPGIQIIGAQPEEGSRIPGIRKWPQEYLPKIYDASTVDELVYVGQDNAEDMCRRLAREEGI 256
                                                     *************************************************************** PP

                                       TIGR01138 249 fvGvssGgavaaalrlarelekavvvaiicdrGdrylstgvf 290
                                                     f G+s+ ga + a ++a   ++a +v ++cdrGdrylstgvf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_644 257 FAGISAAGACWVAQQIAARESNATIVFVVCDRGDRYLSTGVF 298
                                                     *****************************************8 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: 6.45
//
[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