Alignments for a candidate for cysK in Pelobacter propionicus DSM 2379

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Pelobacter propionicus DSM 2379

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_011737168.1 PPRO_RS16725 cysteine synthase family protein

Query= BRENDA::A2GMG5
         (299 letters)



>NCBI__GCF_000015045.1:WP_011737168.1
          Length = 305

 Score =  307 bits (786), Expect = 2e-88
 Identities = 156/292 (53%), Positives = 208/292 (71%)

Query: 5   NILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAKAEGKLQPGS 64
           +++  IG+TP+V I  +NPNPKV + AKLEG NP GSVKDR A +MI  A+A G+L    
Sbjct: 5   SLINAIGSTPMVEIISINPNPKVTILAKLEGNNPGGSVKDRPARQMILAAEASGELTREK 64

Query: 65  TIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGADIILTDKKLGTDGA 124
            I+E TSGNTGI LAMI   +GY + +VM   VS+ERR +++A+GA+I+L+     TDGA
Sbjct: 65  IILEPTSGNTGIALAMIAAARGYRIKLVMPACVSVERRGVLEAYGAEIVLSPGCEATDGA 124

Query: 125 IRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWSQTNGTVTHFVAAVGTSGTLM 184
           IR   ++  + P  YF PNQ++N +N +AHY+TTA EI SQT G VTH VA +GT GTLM
Sbjct: 125 IRLAHKIHDDAPETYFMPNQYANPHNALAHYETTAPEIMSQTEGGVTHVVAGMGTGGTLM 184

Query: 185 GVGKNLREKNPNVKIVEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAFAK 244
           G+ +  RE +PNVK++  +P  GH IQGLK+M+EAIVP IY  + +D  I+IE + AF  
Sbjct: 185 GIARYFREVSPNVKVIGIEPMPGHRIQGLKNMQEAIVPPIYNENALDRKIVIEDDPAFET 244

Query: 245 AREIVAKEGIFIGMSSGAAMLAAQKLAEKLDSGVIVVLFADRGEKYLSTKLF 296
           AR + + EG+F GMS GAAM  A +LA +L+SGVIVV+  DRG++YLST LF
Sbjct: 245 ARLLASHEGVFCGMSGGAAMSGALRLAGELESGVIVVILPDRGDRYLSTNLF 296


Lambda     K      H
   0.315    0.133    0.365 

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: 319
Number of extensions: 4
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: 299
Length of database: 305
Length adjustment: 27
Effective length of query: 272
Effective length of database: 278
Effective search space:    75616
Effective search space used:    75616
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 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_011737168.1 PPRO_RS16725 (cysteine synthase family protein)
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.92756.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-112  360.3   0.1   4.7e-112  360.2   0.1    1.0  1  NCBI__GCF_000015045.1:WP_011737168.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015045.1:WP_011737168.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.2   0.1  4.7e-112  4.7e-112       3     299 .]       8     296 ..       6     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 360.2 bits;  conditional E-value: 4.7e-112
                             TIGR01136   3 eliGntPlvrln.lseelkaevlvKlEsrnPsgSvKdRialsmildAekrgllkkgktiieatSGNtGiaLAm 74 
                                           ++iG+tP+v++  ++++ k+++l+KlE++nP+gSvKdR+a +mil Ae++g+l+++k i+e+tSGNtGiaLAm
  NCBI__GCF_000015045.1:WP_011737168.1   8 NAIGSTPMVEIIsINPNPKVTILAKLEGNNPGGSVKDRPARQMILAAEASGELTREKIILEPTSGNTGIALAM 80 
                                           68********99999********************************************************** PP

                             TIGR01136  75 vaaakgyklilvmpetmslERrkllkayGaelvlteaeegmkgaiekakelaeeepekyvllkqfeNpaNpea 147
                                           +aaa+gy++ lvmp+ +s+ERr +l+ayGae+vl+++ e ++gai+ a+++ ++ pe+y++++q++Np+N  a
  NCBI__GCF_000015045.1:WP_011737168.1  81 IAAARGYRIKLVMPACVSVERRGVLEAYGAEIVLSPGCEATDGAIRLAHKIHDDAPETYFMPNQYANPHNALA 153
                                           ************************************************************************* PP

                             TIGR01136 148 HrkttgpEilkdtdgkidafvagvGtgGtitGvgrvlkekkpnvkivavePaespvlsegkpgphkiqgigag 220
                                           H++tt+pEi+ +t+g ++++vag+GtgGt++G++r+++e +pnvk++++eP+ ++  ++g      +++++++
  NCBI__GCF_000015045.1:WP_011737168.1 154 HYETTAPEIMSQTEGGVTHVVAGMGTGGTLMGIARYFREVSPNVKVIGIEPMPGHR-IQG------LKNMQEA 219
                                           ******************************************************99.778......8****** PP

                             TIGR01136 221 fiPkildeelldevikvededaietarrlakeegilvGiSsGaavaaalkvakklekedkkivvilpdagerY 293
                                           ++P i++e+ ld+ i +ed+ a+etar la++eg+++G+S Gaa+  al++a +le  + +ivvilpd+g+rY
  NCBI__GCF_000015045.1:WP_011737168.1 220 IVPPIYNENALDRKIVIEDDPAFETARLLASHEGVFCGMSGGAAMSGALRLAGELE--SGVIVVILPDRGDRY 290
                                           *******************************************************8..59************* PP

                             TIGR01136 294 Lstelf 299
                                           Lst+lf
  NCBI__GCF_000015045.1:WP_011737168.1 291 LSTNLF 296
                                           *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (305 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.67
//
[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