Alignments for a candidate for cysK in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Desulfobacter vibrioformis DSM 8776

Align cysteine synthase (EC 2.5.1.47); L-3-cyanoalanine synthase (EC 4.4.1.9) (characterized)
to candidate WP_035238797.1 Q366_RS10715 cysteine synthase A

Query= BRENDA::Q84IF9
         (308 letters)



>NCBI__GCF_000745975.1:WP_035238797.1
          Length = 313

 Score =  269 bits (687), Expect = 7e-77
 Identities = 142/300 (47%), Positives = 191/300 (63%), Gaps = 2/300 (0%)

Query: 6   NSITELIGDTPAVKLNRIVDEDSADVYLKLEFMNPGSSVKDRIALAMIEAAEKAGKLKPG 65
           N I   IG TP  ++  +   D  ++Y K E++NPG S+KDR+AL +IE AEK G+LK G
Sbjct: 4   NEILNQIGATPMFRIG-LGGNDDMNIYAKAEYLNPGGSIKDRVALFIIEQAEKKGRLKKG 62

Query: 66  DTIVEPTSGNTGIGLAMVAAAKGYKAVLVMPDTMSLERRNLLRAYGAELVLTPGAQGMRG 125
            +IVE TSGNTGI +AMV   KGY   ++MP+ MS ER+ ++RA  AEL+LTP  + + G
Sbjct: 63  MSIVEATSGNTGIAVAMVGLVKGYDVRIIMPENMSDERKKMIRALNAELILTPPEKNVAG 122

Query: 126 PIAKAEELVREH-GYFMPQQFKNEANPEIHRLTTGKEIVEQMGDQLDAFVAGVGTGGTTT 184
            + K +E++ E    F+P QF+N  N   H L+TG EI + M   +D FV+G+G+GGT  
Sbjct: 123 AVEKLKEIMAEDDNIFVPDQFENHDNSMSHYLSTGPEIWKNMNGHVDIFVSGLGSGGTLM 182

Query: 185 GAGKVLREAYPNIKIYAVEPADSPVLSGGKPGPHKIQGIGAGFVPDILDTSIYDGVITVT 244
           G GK L+E  P I I AVEP ++  L G +PG HKI+GIG GFVP I+DTS+ D VI V 
Sbjct: 183 GTGKYLKEKNPEIMIVAVEPKNASALLGHEPGLHKIEGIGDGFVPSIVDTSLIDNVIEVD 242

Query: 245 TEEAFAAARRAAREEGILGGISSGAAIHAALKVAKELGKGKKVLAIIPSNGERYLSTPLY 304
            + A    R  A ++G L GISSGA + AAL++    GK K +  I P   ERY ST L+
Sbjct: 243 DDSAVEMTRWLASKQGFLVGISSGANVCAALEMRHLFGKDKNIATIFPDGAERYFSTALF 302


Lambda     K      H
   0.314    0.134    0.374 

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: 257
Number of extensions: 6
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: 313
Length adjustment: 27
Effective length of query: 281
Effective length of database: 286
Effective search space:    80366
Effective search space used:    80366
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: 48 (23.1 bits)

Align candidate WP_035238797.1 Q366_RS10715 (cysteine synthase A)
to HMM TIGR01136 (cysteine synthase (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/TIGR01136.hmm
# target sequence database:        /tmp/gapView.958537.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01136  [M=299]
Accession:   TIGR01136
Description: cysKM: cysteine synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-117  377.2   0.1   3.5e-117  377.0   0.1    1.0  1  NCBI__GCF_000745975.1:WP_035238797.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745975.1:WP_035238797.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.0   0.1  3.5e-117  3.5e-117       2     299 .]       7     302 ..       6     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 377.0 bits;  conditional E-value: 3.5e-117
                             TIGR01136   2 eeliGntPlvrlnlseelkaevlvKlEsrnPsgSvKdRialsmildAekrgllkkgktiieatSGNtGiaLAm 74 
                                            + iG tP+ r+ l  + ++++++K E+ nP+gS+KdR+al +i++Aek+g lkkg  i+eatSGNtGia+Am
  NCBI__GCF_000745975.1:WP_035238797.1   7 LNQIGATPMFRIGLGGNDDMNIYAKAEYLNPGGSIKDRVALFIIEQAEKKGRLKKGMSIVEATSGNTGIAVAM 79 
                                           578********************************************************************** PP

                             TIGR01136  75 vaaakgyklilvmpetmslERrkllkayGaelvlteaeegmkgaiekakelaeeepekyvllkqfeNpaNpea 147
                                           v+  kgy + ++mpe+ms ER+k+++a+ ael+lt++e+   ga+ek ke+++e+ +++++++qfeN +N  +
  NCBI__GCF_000745975.1:WP_035238797.1  80 VGLVKGYDVRIIMPENMSDERKKMIRALNAELILTPPEKNVAGAVEKLKEIMAED-DNIFVPDQFENHDNSMS 151
                                           ****************************************************997.5788************* PP

                             TIGR01136 148 HrkttgpEilkdtdgkidafvagvGtgGtitGvgrvlkekkpnvkivavePaespvlsegkpgphkiqgigag 220
                                           H+ +tgpEi+k+++g++d+fv+g+G gGt++G+g++lkek+p++ ivaveP+++++l + +pg hki+gig+g
  NCBI__GCF_000745975.1:WP_035238797.1 152 HYLSTGPEIWKNMNGHVDIFVSGLGSGGTLMGTGKYLKEKNPEIMIVAVEPKNASALLGHEPGLHKIEGIGDG 224
                                           ************************************************************************* PP

                             TIGR01136 221 fiPkildeelldevikvededaietarrlakeegilvGiSsGaavaaalkvakklekedkkivvilpdagerY 293
                                           f+P+i d++l+d+vi+v+d+ a+e++r la+++g lvGiSsGa+v aal++ +    +dk+i +i+pd +erY
  NCBI__GCF_000745975.1:WP_035238797.1 225 FVPSIVDTSLIDNVIEVDDDSAVEMTRWLASKQGFLVGISSGANVCAALEMRHLFG-KDKNIATIFPDGAERY 296
                                           ***************************************************99998.7*************** PP

                             TIGR01136 294 Lstelf 299
                                           +st+lf
  NCBI__GCF_000745975.1:WP_035238797.1 297 FSTALF 302
                                           *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (313 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: 00:00:00.00
# Mc/sec: 15.78
//
[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