Alignments for a candidate for tpi in Chlorobium limicola DSM 245

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Chlorobium limicola DSM 245

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012466585.1 CLIM_RS08420 triose-phosphate isomerase

Query= SwissProt::Q8XKU1
         (248 letters)



>NCBI__GCF_000020465.1:WP_012466585.1
          Length = 251

 Score =  239 bits (609), Expect = 5e-68
 Identities = 129/247 (52%), Positives = 161/247 (65%), Gaps = 4/247 (1%)

Query: 2   RTPIIAGNWKMHYTIDEAVKLVEELKPLVKD--AKCEVVVCPTFVCLDAVKKAVEGTNIK 59
           RT I+AGNWKM+ TI E+V+L   +   +    + CE  + PT   L    K +   ++ 
Sbjct: 3   RTNIVAGNWKMNLTIAESVELASAVIAELGSGFSGCEAGIAPTCPALFETGKLLASGSLF 62

Query: 60  VGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAHN 119
           + AQN H+E  GAFTGE++ RM+      YVIIGHSERR+ F ETDE  N+KV  A    
Sbjct: 63  LAAQNCHYENDGAFTGEVSARMILGAGCTYVIIGHSERRQLFGETDEIVNRKVSKALQEG 122

Query: 120 LTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTATS 179
           L  ILC GETLE+RE G T DV+  Q+ A L G+       +VIAYEP+WAIGTGKTA+S
Sbjct: 123 LRVILCVGETLEEREGGITGDVVTRQVKAGLAGIAG--IGDLVIAYEPVWAIGTGKTASS 180

Query: 180 DQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLVA 239
           +QA E  A IR  V+E++G E AD +RIQYGGSVKP+  AE  A  DIDG L+GGASL A
Sbjct: 181 EQAQEVHALIRKTVSELYGAEAADGLRIQYGGSVKPSNAAELFAMPDIDGGLIGGASLNA 240

Query: 240 ADFAQIV 246
           ADFA IV
Sbjct: 241 ADFAAIV 247


Lambda     K      H
   0.316    0.131    0.376 

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: 170
Number of extensions: 5
Number of successful extensions: 3
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: 248
Length of database: 251
Length adjustment: 24
Effective length of query: 224
Effective length of database: 227
Effective search space:    50848
Effective search space used:    50848
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: 46 (22.3 bits)

Align candidate WP_012466585.1 CLIM_RS08420 (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.9656.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.4e-64  204.0   0.8    1.7e-64  203.8   0.8    1.0  1  lcl|NCBI__GCF_000020465.1:WP_012466585.1  CLIM_RS08420 triose-phosphate is


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012466585.1  CLIM_RS08420 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.8   0.8   1.7e-64   1.7e-64       1     227 [.       6     240 ..       6     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: 203.8 bits;  conditional E-value: 1.7e-64
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeev.aseagvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 
                                               +v +n+K+n ++ +  ++ + + +e+ ++ +g+e ++ap    l    + +    + +aAqn++  + G
  lcl|NCBI__GCF_000020465.1:WP_012466585.1   6 IVAGNWKMNLTIAESVELASAVIAELgSGFSGCEAGIAPTCPALFETGKLLAsGSLFLAAQNCHYENDG 74 
                                               699********99887777777777626789********9988877666665489************** PP

                                 TIGR00419  68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136
                                               aftGe+sA m+  +G+ +v+igHsErR l+ e+de+++ kv+++ + gl++++Cvgetleere + t +
  lcl|NCBI__GCF_000020465.1:WP_012466585.1  75 AFTGEVSARMILGAGCTYVIIGHSERRQLFGETDEIVNRKVSKALQEGLRVILCVGETLEEREGGITGD 143
                                               ********************************************************************* PP

                                 TIGR00419 137 nvattaaa.aA....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGa 199
                                               +v+++ +a  A    + + v+A+EPv++iGtGk++s  +a++v++ +r  +++   +e a+  r++yG+
  lcl|NCBI__GCF_000020465.1:WP_012466585.1 144 VVTRQVKAgLAgiagIGDLVIAYEPVWAIGTGKTASSEQAQEVHALIRKTVSElYGAEAADGLRIQYGG 212
                                               **99987732355579999*****************************999997889************ PP

                                 TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227
                                               sv+ +++ael+a +d+dG L+++a+l a
  lcl|NCBI__GCF_000020465.1:WP_012466585.1 213 SVKPSNAAELFAMPDIDGGLIGGASLNA 240
                                               *************************987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.44
//
[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