GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Williamsia sterculiae CPCC 203464

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_076477793.1 BW971_RS06720 triose-phosphate isomerase

Query= BRENDA::P9WG43
         (261 letters)



>NCBI__GCF_900156495.1:WP_076477793.1
          Length = 262

 Score =  404 bits (1039), Expect = e-118
 Identities = 199/260 (76%), Positives = 223/260 (85%)

Query: 2   SRKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGDK 61
           +R PLIAGNWKMNLNH EAIALVQKIAF+LP KY+D+VDV V+PPFTD+RSVQT+VDGDK
Sbjct: 3   NRTPLIAGNWKMNLNHLEAIALVQKIAFALPAKYFDKVDVTVLPPFTDIRSVQTVVDGDK 62

Query: 62  LRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATA 121
           L LTYGAQDLS HDSGAYTGD+SGAFLAKLGCSYVVVGHSERRT H E D +VAAKA  A
Sbjct: 63  LLLTYGAQDLSQHDSGAYTGDISGAFLAKLGCSYVVVGHSERRTLHGETDEIVAAKAKAA 122

Query: 122 LKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTGR 181
           + HG+ PIVCIGE L+VREAG HVAH + Q++GSLAGL AEQIG  V+AYEPVWAIGTGR
Sbjct: 123 IDHGIVPIVCIGEPLEVREAGEHVAHCVAQVKGSLAGLSAEQIGRTVLAYEPVWAIGTGR 182

Query: 182 VASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGA 241
           VASA DAQEVCAA+R  +A LA   +AD VRVLYGGSV +KNVG++V + DVDG LVGGA
Sbjct: 183 VASADDAQEVCAAVRDAIAQLADQAVADEVRVLYGGSVGSKNVGELVGKPDVDGALVGGA 242

Query: 242 SLDGEHFATLAAIAAGGPLP 261
           SL  + FATL AIAAGGPLP
Sbjct: 243 SLKSDEFATLCAIAAGGPLP 262


Lambda     K      H
   0.318    0.135    0.393 

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: 300
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: 261
Length of database: 262
Length adjustment: 25
Effective length of query: 236
Effective length of database: 237
Effective search space:    55932
Effective search space used:    55932
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_076477793.1 BW971_RS06720 (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.793203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.2e-59  187.9   1.7    1.4e-59  187.7   1.7    1.0  1  NCBI__GCF_900156495.1:WP_076477793.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900156495.1:WP_076477793.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.7   1.7   1.4e-59   1.4e-59       1     228 []       7     247 ..       7     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 187.7 bits;  conditional E-value: 1.4e-59
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.se..iqvaAqnvdavksGa 68 
                                           l+ +n+K+n    +   +v+k+a  +  +  ++v v+v ppf d++ v+  v+  +  ++ +Aq++  ++sGa
  NCBI__GCF_900156495.1:WP_076477793.1   7 LIAGNWKMNLNHLEAIALVQKIAFALPAKyfDKVDVTVLPPFTDIRSVQTVVDgDKllLTYGAQDLSQHDSGA 79 
                                           689********99**********98866534799**************99999544225668*********** PP

                             TIGR00419  69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti.nnvat 140
                                           +tG+is + l+ lG+ +v++gHsErR+l+ e+de++++k   + + g+ ++vC+ge le rea++++   va+
  NCBI__GCF_900156495.1:WP_076477793.1  80 YTGDISGAFLAKLGCSYVVVGHSERRTLHGETDEIVAAKAKAAIDHGIVPIVCIGEPLEVREAGEHVaHCVAQ 152
                                           **************************************************************99987356888 PP

                             TIGR00419 141 taaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaed 206
                                            ++  A      +   v+A+EPv++iGtG+++s  +a++v + vrd +++ +++ va++vrvlyG+sv +++ 
  NCBI__GCF_900156495.1:WP_076477793.1 153 VKGSLAglsaeqIGRTVLAYEPVWAIGTGRVASADDAQEVCAAVRDAIAQlADQAVADEVRVLYGGSVGSKNV 225
                                           888888988898999***********************************9********************** PP

                             TIGR00419 207 aelaaqldvdGvLlasavlkae 228
                                            el+ ++dvdG+L+++a+lk++
  NCBI__GCF_900156495.1:WP_076477793.1 226 GELVGKPDVDGALVGGASLKSD 247
                                           ********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (262 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: 12.79
//
[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:

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:

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:

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:

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