GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Marinobacter adhaerens HP15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF3129 HP15_3071 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Marino:GFF3129
          Length = 252

 Score =  218 bits (556), Expect = 7e-62
 Identities = 119/252 (47%), Positives = 160/252 (63%), Gaps = 3/252 (1%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVA-GCAVAIAPPEMYIDMAKREAEGSHI 59
           MR  +V GNWK+NGS+ +   LVS++R + A +  G  V I PP +Y+      A G  +
Sbjct: 1   MRRKIVAGNWKMNGSKDLAQTLVSDVRSQAASLDNGVEVVIIPPAIYVPDVVASA-GDVL 59

Query: 60  MLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
            +G QNV    SGA+TGE SA M  D G QY ++GHSERR    E+D  +A+K   +   
Sbjct: 60  SVGVQNVAQWASGAYTGEISADMALDQGCQYALVGHSERRQLFAETDAAVAEKVGRILAS 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL  ++C+GET  E EAGK E V A Q+ A L T  +  ++  V+AYEPVWAIGTGK+AT
Sbjct: 120 GLQAMVCVGETLEEREAGKAETVVAAQVKAGLATVASEQWQRVVVAYEPVWAIGTGKTAT 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
              AQA+H  IR  ++++ A  A ++ + YGGSV A NAA LFA+PDIDG L+GGASLKA
Sbjct: 180 AQDAQAMHASIRQVLSEMGAP-ANEISLLYGGSVKADNAAALFAEPDIDGGLIGGASLKA 238

Query: 240 DAFAVIVKAAEA 251
           + F  I ++  A
Sbjct: 239 EDFVSICRSVPA 250


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: 158
Number of extensions: 7
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: 255
Length of database: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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: 47 (22.7 bits)

Align candidate GFF3129 HP15_3071 (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.1068733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    3.2e-67  212.7   7.3    3.7e-67  212.5   7.3    1.0  1  FitnessBrowser__Marino:GFF3129  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF3129  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   7.3   3.7e-67   3.7e-67       1     228 []       5     239 ..       5     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 3.7e-67
                       TIGR00419   1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeisAeml 78 
                                     +v +n+K+n+s    +++v++++ + as  +gvev++ pp ++++ v+  +   ++v+ qnv    sGa+tGeisA+m+
  FitnessBrowser__Marino:GFF3129   5 IVAGNWKMNGSKDLAQTLVSDVRSQAASlDNGVEVVIIPPAIYVPDVVASAGDVLSVGVQNVAQWASGAYTGEISADMA 83 
                                     699*********************99983569********************9************************** PP

                       TIGR00419  79 kdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa.aA......lepd 150
                                      d G+++ l+gHsErR l++e+d  +++kv r+ + gl+++vCvgetleerea++   +va + +a  A      ++ +
  FitnessBrowser__Marino:GFF3129  84 LDQGCQYALVGHSERRQLFAETDAAVAEKVGRILASGLQAMVCVGETLEEREAGKAETVVAAQVKAgLAtvaseqWQRV 162
                                     ****************************************************99999999888766233677999**** PP

                       TIGR00419 151 vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228
                                     vvA+EPv++iGtGk+++  +a+++++s+r+ l++  +  a+++++lyG+sv+a ++a l+a++d+dG L+++a+lkae
  FitnessBrowser__Marino:GFF3129 163 VVAYEPVWAIGTGKTATAQDAQAMHASIRQVLSEMGAP-ANEISLLYGGSVKADNAAALFAEPDIDGGLIGGASLKAE 239
                                     *****************************888876665.6789*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (252 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: 14.65
//
[ok]

This GapMind analysis is from Apr 09 2024. 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