Alignments for a candidate for tpi in Desulfovibrio gracilis DSM 16080

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Desulfovibrio gracilis DSM 16080

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_078716775.1 B5D49_RS06130 triose-phosphate isomerase

Query= BRENDA::A8B3A8
         (249 letters)



>NCBI__GCF_900167125.1:WP_078716775.1
          Length = 251

 Score =  181 bits (458), Expect = 2e-50
 Identities = 107/248 (43%), Positives = 140/248 (56%), Gaps = 10/248 (4%)

Query: 8   VGGNWKMHGSKNSIRDICNTLKG---ASLDPNVEVIVACPAPYLDYCRSLLP--PSVALA 62
           +  NWKM+ + N  RD  + L       L  N EV++  P   L      L   P +A  
Sbjct: 5   MAANWKMYKTWNQARDTASELAQNIRGQLPENREVLIFPPFTALKGVAEALQNEPGMAAG 64

Query: 63  AQNCYKVEQGAFTGEISPGMIKDCGGQWVILGHSERRHVFKEDDVLIGEKIKHALESGLN 122
           AQN Y   +GAFTGEISP M+ D G  WV+ GHSERRHV  ED+  +G K   AL + LN
Sbjct: 65  AQNMYPAAEGAFTGEISPDMLLDVGASWVLTGHSERRHVLGEDNAFVGRKTAFALNNNLN 124

Query: 123 VIACIGELLEDREAGRTEEVCFRQIKHIASNVK---DWSKVVIAYEPVWAIGTGKTATPD 179
           VI CIGEL+E+R A R EEV   Q++   + +        +VIAYEPVWAIGTG+ A PD
Sbjct: 125 VILCIGELIEERRADRVEEVLSEQLEAGLAEIPVGLTSDSLVIAYEPVWAIGTGEVAGPD 184

Query: 180 QAQEVHSKVRNWLSTNVSADVASKVRIQYGGSVNAGNCKELGRKPDIDGFLVGGASLKPE 239
           +    H+ VR  +   +   +AS++ I YGGSV   N   +    ++DG LVGGASL  E
Sbjct: 185 EIATTHTFVRKKIE-ELLPSIASEISILYGGSVKPDNISAIMTLDNVDGVLVGGASLTAE 243

Query: 240 -FVQIINA 246
            F +I+ A
Sbjct: 244 SFSKIVLA 251


Lambda     K      H
   0.318    0.135    0.418 

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: 193
Number of extensions: 9
Number of successful extensions: 4
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: 249
Length of database: 251
Length adjustment: 24
Effective length of query: 225
Effective length of database: 227
Effective search space:    51075
Effective search space used:    51075
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: 46 (22.3 bits)

Align candidate WP_078716775.1 B5D49_RS06130 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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/TIGR00419.hmm
# target sequence database:        /tmp/gapView.20746.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-52  164.6   0.0    1.8e-52  164.4   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078716775.1  B5D49_RS06130 triose-phosphate i


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078716775.1  B5D49_RS06130 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4   0.0   1.8e-52   1.8e-52       2     228 .]       5     243 ..       4     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 1.8e-52
                                 TIGR00419   2 viinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve..seiqvaAqnvdavks 66 
                                               +  n+K+  + ++     ++la+++ ++  ++ ev + ppf  l+ v+++++  + +  +Aqn+     
  lcl|NCBI__GCF_900167125.1:WP_078716775.1   5 MAANWKMYKTWNQARDTASELAQNIRGQlpENREVLIFPPFTALKGVAEALQnePGMAAGAQNMYPAAE 73 
                                               578***9999999999999999999886226789****************9866779999********* PP

                                 TIGR00419  67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135
                                               GaftGeis +ml d+Ga +vl gHsErR +l e + +++ k a + + +l++++C+ge  eer a r  
  lcl|NCBI__GCF_900167125.1:WP_078716775.1  74 GAFTGEISPDMLLDVGASWVLTGHSERRHVLGEDNAFVGRKTAFALNNNLNVILCIGELIEERRADRVE 142
                                               ****************************************************************99988 PP

                                 TIGR00419 136 nnvattaaaaA........lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvl 196
                                               +++ ++ +a           ++ v+A+EPv++iGtG ++ + e    + +vr  +++  + +a ++++l
  lcl|NCBI__GCF_900167125.1:WP_078716775.1 143 EVLSEQLEAGLaeipvgltSDSLVIAYEPVWAIGTGEVAGPDEIATTHTFVRKKIEELLPSIASEISIL 211
                                               888888666434899995555669********************************************* PP

                                 TIGR00419 197 yGasvtaaedaelaaqldvdGvLlasavlkae 228
                                               yG+sv+  +    +   +vdGvL+++a+l ae
  lcl|NCBI__GCF_900167125.1:WP_078716775.1 212 YGGSVKPDNISAIMTLDNVDGVLVGGASLTAE 243
                                               ******999999888889***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (251 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: 9.59
//
[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 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