GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Shewanella loihica PV-4

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 5207770 Shew_0291 branched-chain amino acid aminotransferase (RefSeq)

Query= BRENDA::P0AB80
         (309 letters)



>FitnessBrowser__PV4:5207770
          Length = 307

 Score =  429 bits (1102), Expect = e-125
 Identities = 202/305 (66%), Positives = 246/305 (80%)

Query: 1   MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60
           M  K A+ IWFNGE++ W DAKVHVMSHALHYGTSVFEGIR YD+ +GP  FR  +H+QR
Sbjct: 1   MAAKTAELIWFNGEIMPWGDAKVHVMSHALHYGTSVFEGIRVYDTPQGPAGFRLTDHVQR 60

Query: 61  LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120
           L+DSAKIYR PV  S DE M+ACRD+++ N L +AYIRPL+F GDVGMG+ PP     D+
Sbjct: 61  LYDSAKIYRMPVPYSFDETMQACRDIVKSNKLDAAYIRPLVFFGDVGMGITPPKDAKCDL 120

Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180
           ++AAFPWGAYLG  ++E+G+D  V+SWNR APNTIPT AKAGGNYLSSL + +EA+R+G+
Sbjct: 121 MVAAFPWGAYLGEGSMERGVDVAVTSWNRLAPNTIPTGAKAGGNYLSSLQISTEAKRNGF 180

Query: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240
            EGIALDVNG +SEGAG NLF VK   L+TPP T++ L GITRD II LA++LG EV E+
Sbjct: 181 DEGIALDVNGLVSEGAGANLFVVKKNKLYTPPATAAILLGITRDTIITLARDLGYEVVEE 240

Query: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300
            +SRE LYLADE+FM+GTAAEI PVRSVD I+VG G  GPVT+ +Q +FFGLF GET+DK
Sbjct: 241 PMSREFLYLADEIFMTGTAAEIVPVRSVDRIEVGAGGRGPVTQALQASFFGLFNGETQDK 300

Query: 301 WGWLD 305
           WGWL+
Sbjct: 301 WGWLE 305


Lambda     K      H
   0.319    0.136    0.413 

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: 366
Number of extensions: 9
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: 309
Length of database: 307
Length adjustment: 27
Effective length of query: 282
Effective length of database: 280
Effective search space:    78960
Effective search space used:    78960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 5207770 Shew_0291 (branched-chain amino acid aminotransferase (RefSeq))
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.137642.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
     1e-132  427.8   0.0   1.1e-132  427.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207770  Shew_0291 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207770  Shew_0291 branched-chain amino acid aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.7   0.0  1.1e-132  1.1e-132       1     296 [.      10     305 ..      10     307 .] 1.00

  Alignments for each domain:
  == domain 1  score: 427.7 bits;  conditional E-value: 1.1e-132
                        TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkevl 78 
                                      w++Ge++++ dakvhv++halhYGt+vfeGiR+Y+t++g+a frl++hv+Rlydsaki+r+++pys +e ++++++++
  lcl|FitnessBrowser__PV4:5207770  10 WFNGEIMPWGDAKVHVMSHALHYGTSVFEGIRVYDTPQGPAGFRLTDHVQRLYDSAKIYRMPVPYSFDETMQACRDIV 87 
                                      9***************************************************************************** PP

                        TIGR01122  79 rknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnY 156
                                      ++n+l+ aYiRplv+ G+ ++g++p+ d+k ++++aa++wgaylge ++e+G++v v+s++r a+n+ipt aka+gnY
  lcl|FitnessBrowser__PV4:5207770  88 KSNKLDAAYIRPLVFFGDVGMGITPPKDAKCDLMVAAFPWGAYLGEGSMERGVDVAVTSWNRLAPNTIPTGAKAGGNY 165
                                      ****************************************************************************** PP

                        TIGR01122 157 lnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeeris 234
                                      l+sl + +ea+r+G+de+i+Ld +G v+eG+G n+f+vk+++l+tPp + +iL gitrd++i+la++lg+ev+ee++s
  lcl|FitnessBrowser__PV4:5207770 166 LSSLQISTEAKRNGFDEGIALDVNGLVSEGAGANLFVVKKNKLYTPPATAAILLGITRDTIITLARDLGYEVVEEPMS 243
                                      ****************************************************************************** PP

                        TIGR01122 235 reelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlt 296
                                      re ly+aDe+f+tGtaae++P+r+vD +++g+g rGpvt+ lq +ff l++g+t++k++wl+
  lcl|FitnessBrowser__PV4:5207770 244 REFLYLADEIFMTGTAAEIVPVRSVDRIEVGAGGRGPVTQALQASFFGLFNGETQDKWGWLE 305
                                      ************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (307 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.12
//
[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