Alignments for a candidate for cysK in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Denitrovibrio acetiphilus DSM 12809

Align Cysteine synthase; CSase; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase; EC 2.5.1.47 (characterized)
to candidate WP_013011633.1 DACET_RS11925 cysteine synthase A

Query= SwissProt::Q59966
         (329 letters)



>NCBI__GCF_000025725.1:WP_013011633.1
          Length = 315

 Score =  365 bits (937), Expect = e-106
 Identities = 182/310 (58%), Positives = 231/310 (74%)

Query: 8   FADNSQTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAEQRGLLGP 67
           F +NS TIG+TPLVRLN I       + AK+EGRNPAYSVKCR+ A +I    + G L  
Sbjct: 4   FENNSLTIGETPLVRLNSIQGKYKNNIFAKVEGRNPAYSVKCRVAAGIIKQGIESGKLKE 63

Query: 68  GKELIEPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGVKGMT 127
           G  +IE TSGNTGI L++  AA G  + + MP+TM++ERR ++ A+G +L+LT+G  GM 
Sbjct: 64  GMTIIEATSGNTGIGLSYAGAALGFKVAIIMPDTMTMERRMMMQAFGTELILTDGKLGMK 123

Query: 128 GAVRRAEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVSGVGTGGT 187
           GAV  A+++ A +P++Y L  QFRNPANP IHE TTGPEI+ DT G +D+ VSGVGTGGT
Sbjct: 124 GAVALADEMVAKEPEKYFLANQFRNPANPLIHEATTGPEIFRDTDGKVDVFVSGVGTGGT 183

Query: 188 ITGVSRYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGPHKIQGIGAGFIPENLDLS 247
           ITGVSRY+K  +G  IL+VA EP  SPVISQ     PL+PGPH IQGIGAGFIPE LD+S
Sbjct: 184 ITGVSRYLKNEKGLNILTVAAEPVKSPVISQFIEKQPLQPGPHTIQGIGAGFIPETLDVS 243

Query: 248 LVDQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTIVVVLPDS 307
           L+D VE++ +E A  YARRLA+EEG+ISG+S GAAV AA++  ++ +  GK IVV+LPDS
Sbjct: 244 LIDDVEQIDDENAKEYARRLAREEGIISGVSSGAAVCAAIQAIEKYKLEGKNIVVILPDS 303

Query: 308 GERYLSTALF 317
           GERYLS+ LF
Sbjct: 304 GERYLSSGLF 313


Lambda     K      H
   0.316    0.134    0.378 

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: 360
Number of extensions: 11
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: 329
Length of database: 315
Length adjustment: 28
Effective length of query: 301
Effective length of database: 287
Effective search space:    86387
Effective search space used:    86387
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 WP_013011633.1 DACET_RS11925 (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.3519208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-131  421.6   1.2   9.3e-131  421.5   1.2    1.0  1  NCBI__GCF_000025725.1:WP_013011633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025725.1:WP_013011633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.5   1.2  9.3e-131  9.3e-131       2     298 .]       8     313 ..       7     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 421.5 bits;  conditional E-value: 9.3e-131
                             TIGR01139   2 seliGntPlvrLn.laeeakaevlvkleslnPsssvkdrialamiedaekegllkkgktiveatsGntGiala 73 
                                           s +iG+tPlvrLn ++ + k ++++k+e +nP++svk+r+a+ +i++  ++g+lk+g ti+eatsGntGi+l+
  NCBI__GCF_000025725.1:WP_013011633.1   8 SLTIGETPLVRLNsIQGKYKNNIFAKVEGRNPAYSVKCRVAAGIIKQGIESGKLKEGMTIIEATSGNTGIGLS 80 
                                           569**********889999****************************************************** PP

                             TIGR01139  74 mvaaargykliltmpetmslerrkllkayGaelvLtdgaegmkgaiekaeelveetpnkylllkqfenpanpe 146
                                           + +aa g+k+ ++mp+tm++err++++a+G+el+Ltdg+ gmkga++ a+e+v+++p+ky+l++qf npanp 
  NCBI__GCF_000025725.1:WP_013011633.1  81 YAGAALGFKVAIIMPDTMTMERRMMMQAFGTELILTDGKLGMKGAVALADEMVAKEPEKYFLANQFRNPANPL 153
                                           ************************************************************************* PP

                             TIGR01139 147 ihrkttapeilkdldgkldafvagvGtGGtitGvgevlkekkp.dikvvavePaespvlsgg......kpgph 212
                                           ih++tt+pei++d+dgk+d+fv+gvGtGGtitGv+++lk++k+ +i  va+eP++spv+s+       +pgph
  NCBI__GCF_000025725.1:WP_013011633.1 154 IHEATTGPEIFRDTDGKVDVFVSGVGTGGTITGVSRYLKNEKGlNILTVAAEPVKSPVISQFiekqplQPGPH 226
                                           ******************************************99*****************9999999***** PP

                             TIGR01139 213 kiqGigagfiPkvLdkevidevikvsdeeaietarrlakeeGilvGissGaavaaalkvakkle.kdkkivvi 284
                                            iqGigagfiP+ Ld+++id+v +++de+a e+arrla+eeGi++G+ssGaav aa++  +k + ++k+ivvi
  NCBI__GCF_000025725.1:WP_013011633.1 227 TIQGIGAGFIPETLDVSLIDDVEQIDDENAKEYARRLAREEGIISGVSSGAAVCAAIQAIEKYKlEGKNIVVI 299
                                           **********************************************************9999999******** PP

                             TIGR01139 285 lpdtgerYlstaLf 298
                                           lpd+gerYls  Lf
  NCBI__GCF_000025725.1:WP_013011633.1 300 LPDSGERYLSSGLF 313
                                           **********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (315 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: 00:00:00.00
# Mc/sec: 14.84
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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