GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Moritella dasanensis ArB 0140

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_017222083.1 A923_RS0112890 triose-phosphate isomerase

Query= SwissProt::P50921
         (256 letters)



>NCBI__GCF_000276805.1:WP_017222083.1
          Length = 251

 Score =  262 bits (670), Expect = 4e-75
 Identities = 142/252 (56%), Positives = 171/252 (67%), Gaps = 2/252 (0%)

Query: 1   MRHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAPPALFVDLAERTLTEAGSA 60
           MR  +VMGNWKLN +K  V  L+NGL    +    V+VAV PPA+F+   E  LT A +A
Sbjct: 1   MRQALVMGNWKLNATKASVEALINGLVDAAKDNATVEVAVCPPAVFIPQVE-ALT-ADTA 58

Query: 61  IILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKE 120
           I  GAQ+ D+N SGAFTG+ S  MLKEFG  + ++GHSERR  H ES E VA KFA  +E
Sbjct: 59  ITYGAQDCDVNTSGAFTGENSAVMLKEFGCKYTLVGHSERRVIHGESSEVVADKFAVAQE 118

Query: 121 NGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAA 180
           NGL PVLCIGE+  Q EAGET AV   QL AV+   G+ +L  A+IAYEP+WAIGTGK A
Sbjct: 119 NGLVPVLCIGETLEQFEAGETKAVVEAQLQAVVTKSGITSLNNAVIAYEPVWAIGTGKTA 178

Query: 181 TAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALD 240
           T E AQ IHA IR+ +AE+  AVA  V I YGGSVK  N+A  F Q DIDG LVGGA+LD
Sbjct: 179 TPEIAQEIHAHIRSWLAEQDAAVANKVQILYGGSVKGANSAELFGQADIDGGLVGGASLD 238

Query: 241 AKSFAAIAKAAA 252
           A  F+ +   A+
Sbjct: 239 AVEFSKVIAGAS 250


Lambda     K      H
   0.314    0.130    0.364 

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: 181
Number of extensions: 5
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: 256
Length of database: 251
Length adjustment: 24
Effective length of query: 232
Effective length of database: 227
Effective search space:    52664
Effective search space used:    52664
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 (21.5 bits)
S2: 47 (22.7 bits)

Align candidate WP_017222083.1 A923_RS0112890 (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.3595775.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    9.5e-75  237.3   7.5    1.1e-74  237.1   7.5    1.0  1  NCBI__GCF_000276805.1:WP_017222083.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017222083.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.1   7.5   1.1e-74   1.1e-74       1     227 [.       5     239 ..       5     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 237.1 bits;  conditional E-value: 1.1e-74
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           lv++n+Kln +  +ve +++ l +   ++a vevav pp v+++ v+     + i+ +Aq++d+++sGaftGe
  NCBI__GCF_000276805.1:WP_017222083.1   5 LVMGNWKLNATKASVEALINGLVDAAKDNATVEVAVCPPAVFIPQVEALTAdTAITYGAQDCDVNTSGAFTGE 77 
                                           79********************************************98665599******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138
                                            sA mlk++G+k++l+gHsErR ++ e++e+++ k+a+++e gl +v+C+getle+ e       +  ++++v
  NCBI__GCF_000276805.1:WP_017222083.1  78 NSAVMLKEFGCKYTLVGHSERRVIHGESSEVVADKFAVAQENGLVPVLCIGETLEQFEagetkavVEAQLQAV 150
                                           **********************************************************666665555677777 PP

                             TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                            t+ ++  l+++v+A+EPv++iGtGk++++  a+++++ +r +l++ ++ va++v++lyG+sv++a++ael+ 
  NCBI__GCF_000276805.1:WP_017222083.1 151 VTKSGITSLNNAVIAYEPVWAIGTGKTATPEIAQEIHAHIRSWLAEQDAAVANKVQILYGGSVKGANSAELFG 223
                                           77777777***************************************************************** PP

                             TIGR00419 212 qldvdGvLlasavlka 227
                                           q d+dG L+++a+l a
  NCBI__GCF_000276805.1:WP_017222083.1 224 QADIDGGLVGGASLDA 239
                                           *************976 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: 16.66
//
[ok]

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

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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