GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Psychromonas ossibalaenae JAMM 0738

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_019613419.1 G327_RS0103720 triose-phosphate isomerase

Query= SwissProt::P50921
         (256 letters)



>NCBI__GCF_000381745.1:WP_019613419.1
          Length = 250

 Score =  263 bits (673), Expect = 2e-75
 Identities = 136/251 (54%), Positives = 174/251 (69%), Gaps = 2/251 (0%)

Query: 1   MRHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAPPALFVDLAERTLTEAGSA 60
           MR P+VMGNWKLNG+KE V  L+ GL A  +  T V+VAV PPA+F++     LT A S 
Sbjct: 1   MRTPLVMGNWKLNGTKESVSTLIKGLEAAADAATNVEVAVCPPAIFIEQVAN-LTAANS- 58

Query: 61  IILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKE 120
           I  GAQ+   N  GA+TG+ SP M+KEFGA + ++GHSERR+YH E+D  VA KF  +++
Sbjct: 59  IEFGAQDVSTNVEGAYTGETSPVMVKEFGAKYSLVGHSERRQYHNETDAVVAAKFVAIQK 118

Query: 121 NGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAA 180
           +GL PVLCIGE+  + E   T  V   QL AVI+  G++ALE  +IAYEP+WAIGTGK A
Sbjct: 119 HGLVPVLCIGETLEERETNVTTTVVETQLKAVIDLAGIDALENCVIAYEPVWAIGTGKVA 178

Query: 181 TAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALD 240
           T+E AQ +HA IR+ +AE+S+ VA+ V I YGGSVK  +A   FAQ DIDG LVGGAAL 
Sbjct: 179 TSEQAQEVHAHIRSWLAEQSKVVAEKVQILYGGSVKAASAKELFAQADIDGGLVGGAALI 238

Query: 241 AKSFAAIAKAA 251
            + F  I + A
Sbjct: 239 IEEFVGIIEGA 249


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: 3
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: 250
Length adjustment: 24
Effective length of query: 232
Effective length of database: 226
Effective search space:    52432
Effective search space used:    52432
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: 46 (22.3 bits)

Align candidate WP_019613419.1 G327_RS0103720 (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.1910531.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-72  230.2   9.6    1.6e-72  230.1   9.6    1.0  1  NCBI__GCF_000381745.1:WP_019613419.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019613419.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1   9.6   1.6e-72   1.6e-72       1     225 [.       5     237 ..       5     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 1.6e-72
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           lv++n+Kln++ ++v +++  l++     ++vevav pp ++++ v++    + i+ +Aq+v ++  Ga+tGe
  NCBI__GCF_000381745.1:WP_019613419.1   5 LVMGNWKLNGTKESVSTLIKGLEAAADAATNVEVAVCPPAIFIEQVANLTAaNSIEFGAQDVSTNVEGAYTGE 77 
                                           79***********************999******************99766589******************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145
                                           +s  m+k++Gak++l+gHsErR +++e+d ++++k+  +++ gl +v+C+getleere+  t  +v t+ +a+
  NCBI__GCF_000381745.1:WP_019613419.1  78 TSPVMVKEFGAKYSLVGHSERRQYHNETDAVVAAKFVAIQKHGLVPVLCIGETLEERETNVTTTVVETQLKAV 150
                                           **********************************************************555555555555554 PP

                             TIGR00419 146 A.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                                   le+ v+A+EPv++iGtGk+++  +a++v++ +r +l++ sk vae+v++lyG+sv+aa+++el+a
  NCBI__GCF_000381745.1:WP_019613419.1 151 IdlagidaLENCVIAYEPVWAIGTGKVATSEQAQEVHAHIRSWLAEQSKVVAEKVQILYGGSVKAASAKELFA 223
                                           34444444***************************************************************** PP

                             TIGR00419 212 qldvdGvLlasavl 225
                                           q d+dG L+++a l
  NCBI__GCF_000381745.1:WP_019613419.1 224 QADIDGGLVGGAAL 237
                                           ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (250 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: 15.25
//
[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