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, beta chain; SDH; EC 4.3.1.17; L-serine deaminase; L-SD (uncharacterized)
to candidate WP_075617520.1 GY23_RS01925 L-serine ammonia-lyase, iron-sulfur-dependent, subunit beta

Query= curated2:O34635
         (220 letters)



>NCBI__GCF_001939075.1:WP_075617520.1
          Length = 220

 Score =  296 bits (759), Expect = 2e-85
 Identities = 149/220 (67%), Positives = 179/220 (81%)

Query: 1   MKYRSVFDIIGPVMIGPSSSHTAGAARIGRVARSLFGREPERIIVSFYGSFAETYKGHGT 60
           MK++SVFDIIGPVMIGPSSSHTAGAARIG V R LFGR+P+   V  YGSFAETYKGHGT
Sbjct: 1   MKFKSVFDIIGPVMIGPSSSHTAGAARIGLVTRELFGRQPKWAKVYLYGSFAETYKGHGT 60

Query: 61  DVAIIGGLLDFDTFDERIKTAIQIAEAKGIDIEFRVEDAVPVHPNTAKITISDEKGELEL 120
           D+AIIGGLL FDTFDERIKT+ ++A+   +  EF  E+    HPNTA++ I D+ GE+EL
Sbjct: 61  DIAIIGGLLGFDTFDERIKTSFELAKEASMTYEFIPENGHTEHPNTARLVIGDDAGEMEL 120

Query: 121 TGISIGGGKIEITELNGFELRLSGNHPAILVVHNDKFGTIAGVANVLAKFSINVGHMEVA 180
            G+SIGGGKIEI+ELNGF LRLSGNH AILVVH+D  G+IA VA  LA+ +IN+GHMEV+
Sbjct: 121 IGVSIGGGKIEISELNGFPLRLSGNHSAILVVHDDMPGSIAKVATCLAEQNINIGHMEVS 180

Query: 181 RKDIGQLALMTIEVDQNIDDHILDELSKLPNIIQVTKIAD 220
           RK+ GQ+ALM IEVDQ I+D ++ E++ LP I QVTKIAD
Sbjct: 181 RKEQGQMALMVIEVDQPIEDQVIKEIAMLPYITQVTKIAD 220


Lambda     K      H
   0.319    0.140    0.390 

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: 213
Number of extensions: 6
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: 220
Length of database: 220
Length adjustment: 22
Effective length of query: 198
Effective length of database: 198
Effective search space:    39204
Effective search space used:    39204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate WP_075617520.1 GY23_RS01925 (L-serine ammonia-lyase, iron-sulfur-dependent, subunit beta)
to HMM TIGR00719 (sdaAB: L-serine dehydratase, iron-sulfur-dependent, beta 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/TIGR00719.hmm
# target sequence database:        /tmp/gapView.3778034.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00719  [M=208]
Accession:   TIGR00719
Description: sda_beta: L-serine dehydratase, iron-sulfur-dependent, beta 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-92  295.6   0.5    1.2e-92  295.4   0.5    1.0  1  NCBI__GCF_001939075.1:WP_075617520.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001939075.1:WP_075617520.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.4   0.5   1.2e-92   1.2e-92       1     208 []       1     206 [.       1     206 [. 0.98

  Alignments for each domain:
  == domain 1  score: 295.4 bits;  conditional E-value: 1.2e-92
                             TIGR00719   1 mkdrsvfeviGpvmvGpssshtaGaakiarvarslvsreyervivslyGsfaetykGhGtdvalvGGlldfet 73 
                                           mk +svf++iGpvm+GpssshtaGaa+i+ v+r l++r+++  +v lyGsfaetykGhGtd a++GGll+f+t
  NCBI__GCF_001939075.1:WP_075617520.1   1 MKFKSVFDIIGPVMIGPSSSHTAGAARIGLVTRELFGRQPKWAKVYLYGSFAETYKGHGTDIAIIGGLLGFDT 73 
                                           899********************************************************************** PP

                             TIGR00719  74 dderiktaielakakGldiifrvedlvdnvhpnsvkivisdekGeeeeliGisiGGGkikivelnGielelrG 146
                                           +derikt++elak++ + ++f  e+     hpn++++vi d+ Ge +eliG+siGGGki+i elnG+ l+l+G
  NCBI__GCF_001939075.1:WP_075617520.1  74 FDERIKTSFELAKEASMTYEFIPENGHT-EHPNTARLVIGDDAGE-MELIGVSIGGGKIEISELNGFPLRLSG 144
                                           *********************9999776.9***************.*************************** PP

                             TIGR00719 147 eysaillvynekrGviayvasllakseinveslevkkkdltqlvlltvevdknldeslkdel 208
                                           ++sail+v+++  G ia va+ la+ +in++++ev +k+ +q++l+ +evd+++++++ +e+
  NCBI__GCF_001939075.1:WP_075617520.1 145 NHSAILVVHDDMPGSIAKVATCLAEQNINIGHMEVSRKEQGQMALMVIEVDQPIEDQVIKEI 206
                                           ********************************************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (208 nodes)
Target sequences:                          1  (220 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: 14.65
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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