Alignments for a candidate for cysK in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Bacillus alkalinitrilicus DSM 22532

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_075388449.1 BK574_RS17800 cysteine synthase A

Query= BRENDA::P37887
         (308 letters)



>NCBI__GCF_002019605.1:WP_075388449.1
          Length = 307

 Score =  484 bits (1247), Expect = e-142
 Identities = 240/307 (78%), Positives = 277/307 (90%), Gaps = 1/307 (0%)

Query: 2   VRVANSITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGK 61
           +RVANSIT+LIG TP+VKLNR+  E +AD+YLKLEY NPGSSVKDRI LAMIEAAEK+G+
Sbjct: 1   MRVANSITDLIGQTPLVKLNRIVPEGAADIYLKLEYFNPGSSVKDRIALAMIEAAEKDGR 60

Query: 62  LKAGNTIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAE 121
           LK  +TI+EPTSGNTGIGLAMVA+AKG K  LVMP+TMS+ERRNLLRAYGAELVLTPG E
Sbjct: 61  LKPEDTIVEPTSGNTGIGLAMVASAKGYKTKLVMPETMSIERRNLLRAYGAELVLTPGPE 120

Query: 122 GMKGAIKKAEELAEKHGYFVPQQFNNPSNPEIHRQTTGKEIVEQFGDDQLDAFVAGIGTG 181
           GM GAI+KA EL+++ GYF+PQQF N +NPEIHR+TTGKE++EQ  D  +DAF++GIGTG
Sbjct: 121 GMGGAIRKATELSKEDGYFMPQQFENEANPEIHRETTGKELLEQV-DGSVDAFISGIGTG 179

Query: 182 GTITGAGEVLKEAYPSIKIYAVEPSDSPVLSGGKPGPHKIQGIGAGFVPDILNTEVYDEI 241
           GTITGAG +LKE +P +KIYAVEP+DSPVLSGGKPGPHKIQGIGAGFVP IL+T+VYDE+
Sbjct: 180 GTITGAGGLLKENFPELKIYAVEPADSPVLSGGKPGPHKIQGIGAGFVPSILDTKVYDEV 239

Query: 242 FPVKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSNGERYLS 301
             V N++AFEYARRA REEGILGGISSGAAIYAA+QVA+KLG GKKV+AIIPSNGERYLS
Sbjct: 240 IKVTNDQAFEYARRAGREEGILGGISSGAAIYAAIQVAEKLGAGKKVVAIIPSNGERYLS 299

Query: 302 TPLYQFD 308
           TPLYQFD
Sbjct: 300 TPLYQFD 306


Lambda     K      H
   0.313    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: 334
Number of extensions: 9
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: 308
Length of database: 307
Length adjustment: 27
Effective length of query: 281
Effective length of database: 280
Effective search space:    78680
Effective search space used:    78680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_075388449.1 BK574_RS17800 (cysteine synthase 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.15793.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-146  473.8   0.1   1.2e-146  473.6   0.1    1.0  1  lcl|NCBI__GCF_002019605.1:WP_075388449.1  BK574_RS17800 cysteine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_075388449.1  BK574_RS17800 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.6   0.1  1.2e-146  1.2e-146       1     298 []       7     303 ..       7     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 473.6 bits;  conditional E-value: 1.2e-146
                                 TIGR01139   1 iseliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGnt 68 
                                               i++liG+tPlv+Ln ++ e +a++++kle++nP+ssvkdrialamie aek+g lk+++tive+tsGnt
  lcl|NCBI__GCF_002019605.1:WP_075388449.1   7 ITDLIGQTPLVKLNrIVPEGAADIYLKLEYFNPGSSVKDRIALAMIEAAEKDGRLKPEDTIVEPTSGNT 75 
                                               589***********8888899************************************************ PP

                                 TIGR01139  69 GialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllk 137
                                               Gi+lamva+a+gyk  l+mpetms+err+ll+ayGaelvLt+g egm gai+ka el +e++  y++++
  lcl|NCBI__GCF_002019605.1:WP_075388449.1  76 GIGLAMVASAKGYKTKLVMPETMSIERRNLLRAYGAELVLTPGPEGMGGAIRKATELSKEDG--YFMPQ 142
                                               *************************************************************9..99*** PP

                                 TIGR01139 138 qfenpanpeihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkpdikvvavePaespvlsg 206
                                               qfen+anpeihr+tt++e+l+++dg++daf++g+GtGGtitG+g +lke++p++k++avePa+spvlsg
  lcl|NCBI__GCF_002019605.1:WP_075388449.1 143 QFENEANPEIHRETTGKELLEQVDGSVDAFISGIGTGGTITGAGGLLKENFPELKIYAVEPADSPVLSG 211
                                               ********************************************************************* PP

                                 TIGR01139 207 gkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkl 275
                                               gkpgphkiqGigagf+P++Ld++v+devikv++++a+e+arr  +eeGil GissGaa++aa++va+kl
  lcl|NCBI__GCF_002019605.1:WP_075388449.1 212 GKPGPHKIQGIGAGFVPSILDTKVYDEVIKVTNDQAFEYARRAGREEGILGGISSGAAIYAAIQVAEKL 280
                                               ********************************************************************* PP

                                 TIGR01139 276 ekdkkivvilpdtgerYlstaLf 298
                                               +++kk+v+i+p++gerYlst+L+
  lcl|NCBI__GCF_002019605.1:WP_075388449.1 281 GAGKKVVAIIPSNGERYLSTPLY 303
                                               *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (307 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: 10.62
//
[ok]

This GapMind analysis is from Apr 10 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