Alignments for a candidate for sdaB in Paenisporosarcina indica PN2

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Paenisporosarcina indica PN2

Align Probable L-serine dehydratase, alpha chain; SDH; EC 4.3.1.17; L-serine deaminase; L-SD (uncharacterized)
to candidate WP_075617521.1 GY23_RS01930 L-serine ammonia-lyase, iron-sulfur-dependent, subunit alpha

Query= curated2:O34607
         (300 letters)



>NCBI__GCF_001939075.1:WP_075617521.1
          Length = 298

 Score =  455 bits (1171), Expect = e-133
 Identities = 228/288 (79%), Positives = 263/288 (91%)

Query: 1   MFRNVKELIEITKEKQILISDVMIAQEMEVTEKTKEDIFQQMDHNLSVMEAAVQKGLEGV 60
           +FRNVKEL+E+   +  LIS++MI QEM VT +T+EDI  QMD NL+VME AV+KGL+GV
Sbjct: 4   LFRNVKELVELASTENKLISELMIEQEMLVTRRTREDIMNQMDRNLTVMEQAVEKGLKGV 63

Query: 61  TSQTGLTGGDAVKLQAYIRSGKSLSGPLILDAVSKAVATNEVNAAMGTICATPTAGSAGV 120
            S +GLTGGDAV LQ Y++ G +LSG L++DAVSKAVATNEVNAAMGTICATPTAGSAGV
Sbjct: 64  HSTSGLTGGDAVLLQDYMKKGNTLSGNLLIDAVSKAVATNEVNAAMGTICATPTAGSAGV 123

Query: 121 VPGTLFAVKEKLNPTREQMIRFLFTAGAFGFVVANNASISGAAGGCQAEVGSASGMAAAA 180
           VPGTLFAV+ +L+PTREQMIR+LFT+GAFGFVVANNASISGAAGGCQAEVGSA+ MAAAA
Sbjct: 124 VPGTLFAVQNQLHPTREQMIRYLFTSGAFGFVVANNASISGAAGGCQAEVGSAAAMAAAA 183

Query: 181 IVEMAGGTPEQSAEAMAITLKNMLGLVCDPVAGLVEVPCVKRNAMGASNAMIAADMALAG 240
           IVEMAGGTP+QS+EA AIT+KNMLGLVCDPVAGLVEVPCVKRNAMGA+NA++AADMALAG
Sbjct: 184 IVEMAGGTPQQSSEAFAITMKNMLGLVCDPVAGLVEVPCVKRNAMGAANALVAADMALAG 243

Query: 241 ITSRIPCDEVIDAMYKIGQTMPTALRETGQGGLAATPTGRELEKKIFG 288
           +TSRIPCDEVIDAM+KIGQ+MPTAL+ET QGGLAATPTGR L ++IFG
Sbjct: 244 VTSRIPCDEVIDAMFKIGQSMPTALKETAQGGLAATPTGRALAERIFG 291


Lambda     K      H
   0.314    0.129    0.351 

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: 389
Number of extensions: 7
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: 300
Length of database: 298
Length adjustment: 27
Effective length of query: 273
Effective length of database: 271
Effective search space:    73983
Effective search space used:    73983
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_075617521.1 GY23_RS01930 (L-serine ammonia-lyase, iron-sulfur-dependent, subunit alpha)
to HMM TIGR00718 (sdaAA: L-serine dehydratase, iron-sulfur-dependent, alpha subunit (EC 4.3.1.17))

# 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.carbon/TIGR00718.hmm
# target sequence database:        /tmp/gapView.3763668.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00718  [M=300]
Accession:   TIGR00718
Description: sda_alpha: L-serine dehydratase, iron-sulfur-dependent, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-144  467.1  15.1   1.3e-144  466.8  15.1    1.0  1  NCBI__GCF_001939075.1:WP_075617521.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001939075.1:WP_075617521.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.8  15.1  1.3e-144  1.3e-144       1     288 [.       4     291 ..       4     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 466.8 bits;  conditional E-value: 1.3e-144
                             TIGR00718   1 mlrtvkelievtkekqikisdlvleeeikvsektkeeirkkldavldvmeaavqknlesvvsetklidGdakk 73 
                                           ++r+vkel+e++   + +is+l++e+e+ v+++t+e+i++++d +l vme av+k+l++v s  +l++Gda+ 
  NCBI__GCF_001939075.1:WP_075617521.1   4 LFRNVKELVELASTENKLISELMIEQEMLVTRRTREDIMNQMDRNLTVMEQAVEKGLKGVHSTSGLTGGDAVL 76 
                                           59*********************************************************************** PP

                             TIGR00718  74 lqeyirsGkslvGdllldavakavatsevnaamGkivaaptaGsaGvvpatlvavkeklnfdreqiirfllta 146
                                           lq+y++ G +l+G+ll+dav+kavat+evnaamG+i+a+ptaGsaGvvp+tl+av+++l ++req+ir+l+t+
  NCBI__GCF_001939075.1:WP_075617521.1  77 LQDYMKKGNTLSGNLLIDAVSKAVATNEVNAAMGTICATPTAGSAGVVPGTLFAVQNQLHPTREQMIRYLFTS 149
                                           ************************************************************************* PP

                             TIGR00718 147 iaiGfvvakyasiaGaeGGcqaevGsasamaaaalvemlGGtveqaleaaaitlknvlGlvcdpvaGlvevpc 219
                                           +a+Gfvva++asi+Ga+GGcqaevGsa+amaaaa+vem+GGt++q+ ea ait+kn+lGlvcdpvaGlvevpc
  NCBI__GCF_001939075.1:WP_075617521.1 150 GAFGFVVANNASISGAAGGCQAEVGSAAAMAAAAIVEMAGGTPQQSSEAFAITMKNMLGLVCDPVAGLVEVPC 222
                                           ************************************************************************* PP

                             TIGR00718 220 vkrnasGvinaliaadlalaGveslvpfdevviamykvGqsmiealretGlGGlaasktGrklekdilk 288
                                           vkrna+G++nal+aad+alaGv+s++p+dev++am+k+Gqsm++al+et +GGlaa++tGr l   i++
  NCBI__GCF_001939075.1:WP_075617521.1 223 VKRNAMGAANALVAADMALAGVTSRIPCDEVIDAMFKIGQSMPTALKETAQGGLAATPTGRALAERIFG 291
                                           ******************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (298 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: 17.82
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 2024 update 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

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 catabolism of small carbon sources