GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dechlorosoma suillum PS

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Dsui_3052 Dsui_3052 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__PS:Dsui_3052
          Length = 241

 Score =  240 bits (613), Expect = 2e-68
 Identities = 128/238 (53%), Positives = 163/238 (68%), Gaps = 3/238 (1%)

Query: 12  LNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQNVDLNLS 71
           L  +R ++  +V+ + K LA    CAV +  P  Y+  A++E   + +  GAQN+   +S
Sbjct: 5   LAANRSLLQGVVAGV-KGLAAAVECAVCVPYP--YLAQAQQELAKTEVSWGAQNLSEQVS 61

Query: 72  GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETE 131
           GAFTGE SAAMLKD G +Y+I+GHSERR  + E D L+AKKF      GL P+LC+GET 
Sbjct: 62  GAFTGEVSAAMLKDFGCRYVIVGHSERRALYGEDDGLVAKKFKQALAGGLVPILCVGETL 121

Query: 132 AENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQAVHKFIR 191
           A+ E+G+  EV A Q+DAVL   G   F GAV+AYEPVWAIGTG +A+PAQAQAVH+ IR
Sbjct: 122 AQRESGQAAEVVAAQLDAVLDAAGVEVFAGAVVAYEPVWAIGTGLTASPAQAQAVHEGIR 181

Query: 192 DHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAVIVKAA 249
             +A  +A +A  V + YGGSV A NAAELFA PDIDGALVGGASL A+ F  I +AA
Sbjct: 182 ARLAARNAEVAAGVRVLYGGSVKAGNAAELFAMPDIDGALVGGASLVAEEFVAICRAA 239


Lambda     K      H
   0.316    0.130    0.366 

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: 195
Number of extensions: 9
Number of successful extensions: 2
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: 255
Length of database: 241
Length adjustment: 24
Effective length of query: 231
Effective length of database: 217
Effective search space:    50127
Effective search space used:    50127
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 Dsui_3052 Dsui_3052 (triosephosphate 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.11254.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    4.6e-68  215.5   5.9    5.3e-68  215.2   5.9    1.0  1  lcl|FitnessBrowser__PS:Dsui_3052  Dsui_3052 triosephosphate isomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3052  Dsui_3052 triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.2   5.9   5.3e-68   5.3e-68      30     228 .]      24     230 ..       3     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 5.3e-68
                         TIGR00419  30 agvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeisAemlkdlGakgvligHsErRsllkeadelie 105
                                       a ve av +p+ +l  +++e+  +e++ +Aqn+  + sGaftGe+sA+mlkd+G+++v++gHsErR+l  e d l++
  lcl|FitnessBrowser__PS:Dsui_3052  24 AAVECAVCVPYPYLAQAQQELAkTEVSWGAQNLSEQVSGAFTGEVSAAMLKDFGCRYVIVGHSERRALYGEDDGLVA 100
                                       5688999*************9889***************************************************** PP

                         TIGR00419 106 kkvarlkelglksvvCvgetleere.......aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevve 175
                                       kk+ ++ + gl +++Cvgetl++re       +a ++++v++ a++  + ++vvA+EPv++iGtG ++s+A+a++v+
  lcl|FitnessBrowser__PS:Dsui_3052 101 KKFKQALAGGLVPILCVGETLAQREsgqaaevVAAQLDAVLDAAGVEVFAGAVVAYEPVWAIGTGLTASPAQAQAVH 177
                                       *************************88888887888888888888888***************************** PP

                         TIGR00419 176 ksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228
                                       + +r  l+  ++eva  vrvlyG+sv+a+++ael+a +d+dG+L+++a+l ae
  lcl|FitnessBrowser__PS:Dsui_3052 178 EGIRARLAARNAEVAAGVRVLYGGSVKAGNAAELFAMPDIDGALVGGASLVAE 230
                                       **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (241 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: 9.10
//
[ok]

This GapMind analysis is from Sep 17 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