Alignments for a candidate for cysK in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Sinorhizobium meliloti 1021

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate SMc00421 SMc00421 O-acetylserine sulfhydrylase A

Query= BRENDA::C4ITG6
         (334 letters)



>FitnessBrowser__Smeli:SMc00421
          Length = 322

 Score =  490 bits (1261), Expect = e-143
 Identities = 243/318 (76%), Positives = 279/318 (87%), Gaps = 2/318 (0%)

Query: 18  DAEAAGRGRIYDSILDTIGNTPLVRIDKFARENGVKANLLVKLEFFNPLASVKDRIGLAM 77
           +A   GRGR++ SI +TIG+TP+VR+DK A+E GVKANLL KLEFFNP+ SVKDRIG+AM
Sbjct: 3   EARKPGRGRVFSSITETIGDTPIVRLDKLAKEKGVKANLLAKLEFFNPIGSVKDRIGVAM 62

Query: 78  IEALEKQGKAVPGKTVFVEPTSGNTGIALAFAAAAKGYRLILTMPETMSMERRKLLRLLG 137
           IE+LE QGK  PG+T  VEPTSGNTGIALAF AAAKGYRLILTMPETMS+ERRK+L LLG
Sbjct: 63  IESLEAQGKITPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPETMSVERRKMLTLLG 122

Query: 138 AELVLTEGAKGMKGAIAEAEAIGN--PNAIIPQQFENPANPEIHRLTTAEEIWNDTNGEA 195
           AELVLTEGAKGMKGAIA+A+ +    P+AIIPQQFENPANPEIHR TTAEEIWNDT G  
Sbjct: 123 AELVLTEGAKGMKGAIAKAQELTETLPDAIIPQQFENPANPEIHRTTTAEEIWNDTEGAV 182

Query: 196 DILISGIGTGGTITGVGQVIKARKPSFKVVAVEPKDSPVLSGGAPGPHKIQGLGAGFAPK 255
           DIL+SGIGTGGTITG GQV+KARKPS +V+AVEP++SP+LSGGAPGPHKIQG+GAGFAP 
Sbjct: 183 DILVSGIGTGGTITGAGQVLKARKPSVRVIAVEPEESPILSGGAPGPHKIQGIGAGFAPA 242

Query: 256 TLDTGIYDEIVQISNEDAFTNARLVARLEGIPVGISSGAALAAAIEVGKRSENAGKNIVV 315
            LDT +YDE+V ++  +A   ARLVARLEG+PVGIS+GAAL AAIEVG+R ENAG+NIVV
Sbjct: 243 ILDTSVYDEVVTVNAGEAIEAARLVARLEGVPVGISAGAALQAAIEVGQREENAGRNIVV 302

Query: 316 VIPSFAERYLSTALFEGL 333
           +IPSFAERYLST LFEGL
Sbjct: 303 IIPSFAERYLSTVLFEGL 320


Lambda     K      H
   0.314    0.134    0.373 

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: 395
Number of extensions: 7
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: 334
Length of database: 322
Length adjustment: 28
Effective length of query: 306
Effective length of database: 294
Effective search space:    89964
Effective search space used:    89964
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: 42 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate SMc00421 SMc00421 (O-acetylserine sulfhydrylase A)
to HMM TIGR01139 (cysK: cysteine synthase A (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/TIGR01139.hmm
# target sequence database:        /tmp/gapView.4130.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01139  [M=298]
Accession:   TIGR01139
Description: cysK: cysteine synthase A
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-135  437.5   3.7   1.4e-135  437.3   3.7    1.0  1  lcl|FitnessBrowser__Smeli:SMc00421  SMc00421 O-acetylserine sulfhydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00421  SMc00421 O-acetylserine sulfhydrylase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.3   3.7  1.4e-135  1.4e-135       1     298 []      16     317 ..      16     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 437.3 bits;  conditional E-value: 1.4e-135
                           TIGR01139   1 iseliGntPlvrLn...laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgk.tiveatsGntGia 71 
                                         i+e+iG+tP+vrL+    ++++ka++l+kle++nP +svkdri++amie+ e +g++++g+ t+ve+tsGntGia
  lcl|FitnessBrowser__Smeli:SMc00421  16 ITETIGDTPIVRLDklaKEKGVKANLLAKLEFFNPIGSVKDRIGVAMIESLEAQGKITPGRtTLVEPTSGNTGIA 90 
                                         689**********98545667899************************************879************ PP

                           TIGR01139  72 lamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpe 146
                                         la+vaaa+gy+liltmpetms+errk+l+ +GaelvLt+ga+gmkgai+ka+el+e+ p++  +++qfenpanpe
  lcl|FitnessBrowser__Smeli:SMc00421  91 LAFVAAAKGYRLILTMPETMSVERRKMLTLLGAELVLTEGAKGMKGAIAKAQELTETLPDAI-IPQQFENPANPE 164
                                         ***********************************************************777.************ PP

                           TIGR01139 147 ihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsggkpgphkiqGigagf 221
                                         ihr+tta+ei++d++g++d++v+g+GtGGtitG+g+vlk  kp+++v+aveP+esp+lsgg pgphkiqGigagf
  lcl|FitnessBrowser__Smeli:SMc00421 165 IHRTTTAEEIWNDTEGAVDILVSGIGTGGTITGAGQVLKARKPSVRVIAVEPEESPILSGGAPGPHKIQGIGAGF 239
                                         *************************************************************************** PP

                           TIGR01139 222 iPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvilpdtgerYlst 295
                                          P++Ld++v+dev++v+  eaie ar +a+ eG+ vGis+Gaa+ aa++v +++e ++++ivvi+p+++erYlst
  lcl|FitnessBrowser__Smeli:SMc00421 240 APAILDTSVYDEVVTVNAGEAIEAARLVARLEGVPVGISAGAALQAAIEVGQREEnAGRNIVVIIPSFAERYLST 314
                                         *****************************************************9999****************** PP

                           TIGR01139 296 aLf 298
                                          Lf
  lcl|FitnessBrowser__Smeli:SMc00421 315 VLF 317
                                         *99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (322 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: 8.03
//
[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