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_075385937.1 BK574_RS21905 cysteine synthase A

Query= BRENDA::P37887
         (308 letters)



>NCBI__GCF_002019605.1:WP_075385937.1
          Length = 312

 Score =  348 bits (893), Expect = e-101
 Identities = 187/310 (60%), Positives = 224/310 (72%), Gaps = 3/310 (0%)

Query: 2   VRVANSITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGK 61
           +RV N+I ELIG+TP+VKLN++AD+N A VYLKLE+ NP  SVKDR    MI  AEK+G 
Sbjct: 1   MRVVNNIAELIGHTPLVKLNKIADKNGASVYLKLEFFNPSGSVKDRAAYQMIIQAEKDGL 60

Query: 62  LKAGNTIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAE 121
           LK G TIIEPTSGNTGIGLAM AAA+G KAIL MPDTMS ER N+L+AYGAE+VLT G +
Sbjct: 61  LKPGATIIEPTSGNTGIGLAMNAAARGYKAILTMPDTMSEERINILKAYGAEVVLTEGDK 120

Query: 122 GMKGAIKKAEELAEK-HGYFVPQQFNNPSNPEIHRQTTGKEIVEQFGD--DQLDAFVAGI 178
            M GAI KA ELA+     FVP QF NP+NP+ HR TT  EI E       +L AFVA  
Sbjct: 121 KMPGAIDKAHELAKDIPNSFVPMQFENPANPDAHRYTTAVEIKEALDSIGKKLSAFVAAS 180

Query: 179 GTGGTITGAGEVLKEAYPSIKIYAVEPSDSPVLSGGKPGPHKIQGIGAGFVPDILNTEVY 238
           GTGGTITG GE LK+ YP   ++ VEP+ SPVLSGGKPGPHK+ G   GF+P ILN  VY
Sbjct: 181 GTGGTITGTGEELKKFYPKATVHVVEPAGSPVLSGGKPGPHKLVGTSPGFIPPILNENVY 240

Query: 239 DEIFPVKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSNGER 298
           +EI  +++E+A+  +   AR+EGIL G SSGAA +AAL+VAK L     V+AI    GER
Sbjct: 241 NEIKKIEDEDAYWASIELARKEGILVGPSSGAACFAALEVAKTLSPDDVVVAIACDTGER 300

Query: 299 YLSTPLYQFD 308
           YLST L+ F+
Sbjct: 301 YLSTDLFDFE 310


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: 294
Number of extensions: 13
Number of successful extensions: 3
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: 312
Length adjustment: 27
Effective length of query: 281
Effective length of database: 285
Effective search space:    80085
Effective search space used:    80085
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_075385937.1 BK574_RS21905 (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.6980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-136  438.4   0.0   7.5e-136  438.2   0.0    1.0  1  lcl|NCBI__GCF_002019605.1:WP_075385937.1  BK574_RS21905 cysteine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_075385937.1  BK574_RS21905 cysteine synthase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.2   0.0  7.5e-136  7.5e-136       2     298 .]       8     307 ..       7     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 438.2 bits;  conditional E-value: 7.5e-136
                                 TIGR01139   2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntG 69 
                                               +eliG+tPlv+Ln +a+++ a+v++kle++nPs+svkdr+a++mi +aek+gllk+g ti+e+tsGntG
  lcl|NCBI__GCF_002019605.1:WP_075385937.1   8 AELIGHTPLVKLNkIADKNGASVYLKLEFFNPSGSVKDRAAYQMIIQAEKDGLLKPGATIIEPTSGNTG 76 
                                               799**********9999999************************************************* PP

                                 TIGR01139  70 ialamvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkq 138
                                               i+lam aaargyk+iltmp+tms+er ++lkayGae+vLt+g+++m gai+ka+el+++ pn++ +++q
  lcl|NCBI__GCF_002019605.1:WP_075385937.1  77 IGLAMNAAARGYKAILTMPDTMSEERINILKAYGAEVVLTEGDKKMPGAIDKAHELAKDIPNSF-VPMQ 144
                                               *************************************************************999.**** PP

                                 TIGR01139 139 fenpanpeihrkttapeilkdldgk...ldafvagvGtGGtitGvgevlkekkpdikvvavePaespvl 204
                                               fenpanp++hr tta ei ++ld     l afva+ GtGGtitG+ge lk+  p+ +v++vePa spvl
  lcl|NCBI__GCF_002019605.1:WP_075385937.1 145 FENPANPDAHRYTTAVEIKEALDSIgkkLSAFVAASGTGGTITGTGEELKKFYPKATVHVVEPAGSPVL 213
                                               ******************9987753334***************************************** PP

                                 TIGR01139 205 sggkpgphkiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvak 273
                                               sggkpgphk+ G+++gfiP +L+++v++e+ k++de+a+  + +la++eGilvG ssGaa++aal+vak
  lcl|NCBI__GCF_002019605.1:WP_075385937.1 214 SGGKPGPHKLVGTSPGFIPPILNENVYNEIKKIEDEDAYWASIELARKEGILVGPSSGAACFAALEVAK 282
                                               ********************************************************************* PP

                                 TIGR01139 274 klekdkkivvilpdtgerYlstaLf 298
                                                l++d ++v+i++dtgerYlst+Lf
  lcl|NCBI__GCF_002019605.1:WP_075385937.1 283 TLSPDDVVVAIACDTGERYLSTDLF 307
                                               ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (312 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.14
//
[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