Aligments for a candidate for ilvE in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for ilvE in Phaeobacter inhibens BS107

Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate GFF3358 PGA1_c34110 branched-chain-amino-acid aminotransferase IlvE

Query= metacyc::MONOMER-11914
         (306 letters)



>FitnessBrowser__Phaeo:GFF3358
          Length = 288

 Score =  228 bits (580), Expect = 2e-64
 Identities = 117/265 (44%), Positives = 167/265 (63%), Gaps = 7/265 (2%)

Query: 4   EASGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFD 63
           +  G IW++GEMV W +A VH+LSH +HY SSVFEG R Y       IF+ REH +RL  
Sbjct: 6   DRDGLIWMDGEMVNWRDAKVHILSHAMHYASSVFEGERAYNGK----IFKSREHSERLIA 61

Query: 64  SAKIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGE-MGVHPVNCPVDVAVA 122
           SA+   M +PYT +QI  A  ET++ +GL++ Y+R VV+RG GE MGV     PV +A+A
Sbjct: 62  SAEALDMPMPYTVDQIEAAKEETLKASGLQDAYVRAVVWRGSGEDMGVASAKNPVRMAIA 121

Query: 123 AWEWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEA 182
            W WGAY G   ++ G    ++ W+R +P T+P  AKA G Y+   ++K +A   G  +A
Sbjct: 122 VWGWGAYYGDAKMQ-GAKLDIAEWKRPSPETIPVHAKAAGLYMICTISKHKAEAKGCSDA 180

Query: 183 IMLDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPIT 242
           + +DY GY++E +G NIF V +GE++TP      L GITR +VI + +  G+TVHE  I 
Sbjct: 181 LFMDYRGYVAEATGANIFFVKDGEVHTPK-PDCFLNGITRQTVIGMLKDRGITVHERHIM 239

Query: 243 REMLYIADEAFFTGTAAEITPIRSV 267
            E L   ++ + TGTAAE+TP+  +
Sbjct: 240 PEELDGFEQCWLTGTAAEVTPVGQI 264


Lambda     K      H
   0.320    0.136    0.414 

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: 306
Number of extensions: 18
Number of successful extensions: 5
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: 306
Length of database: 288
Length adjustment: 26
Effective length of query: 280
Effective length of database: 262
Effective search space:    73360
Effective search space used:    73360
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 GFF3358 PGA1_c34110 (branched-chain-amino-acid aminotransferase IlvE)
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.32364.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.4e-89  285.4   0.0    2.7e-89  285.2   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3358  PGA1_c34110 branched-chain-amino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3358  PGA1_c34110 branched-chain-amino-acid aminotransferase IlvE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.2   0.0   2.7e-89   2.7e-89       1     285 [.      12     287 ..      12     288 .] 0.97

  Alignments for each domain:
  == domain 1  score: 285.2 bits;  conditional E-value: 2.7e-89
                          TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtke 76 
                                        w+dGe+v+++dakvh+l+ha+hY ++vfeG RaY++     if+ +eh eRl  sa++l++++py+ +++  +  e
  lcl|FitnessBrowser__Phaeo:GFF3358  12 WMDGEMVNWRDAKVHILSHAMHYASSVFEGERAYNG----KIFKSREHSERLIASAEALDMPMPYTVDQIEAAKEE 83 
                                        9***********************************....9*********************************** PP

                          TIGR01122  77 vlrknnlksaYiRplvyvGa.edlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkak 151
                                        +l++++l++aY+R +v++G+ ed+g+   ++ +v+++ia+w wgay+g+ a  +G k  ++ ++r ++++ip +ak
  lcl|FitnessBrowser__Phaeo:GFF3358  84 TLKASGLQDAYVRAVVWRGSgEDMGVAS-AKNPVRMAIAVWGWGAYYGD-AKMQGAKLDIAEWKRPSPETIPVHAK 157
                                        *******************8458****9.889****************7.7889********************** PP

                          TIGR01122 152 aagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgie 227
                                        aag Y+  ++ k++a ++G  +a+++d  Gyvae +G nif vkdg++ tP+  +  L+gitr++vi ++k++gi+
  lcl|FitnessBrowser__Phaeo:GFF3358 158 AAGLYMICTISKHKAEAKGCSDALFMDYRGYVAEATGANIFFVKDGEVHTPKP-DCFLNGITRQTVIGMLKDRGIT 232
                                        ****************************************************9.99******************** PP

                          TIGR01122 228 vkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlve 285
                                        v+e++i  eel   +  +ltGtaaevtP+ ++   +    ++G++t+ + +a+ +lv+
  lcl|FitnessBrowser__Phaeo:GFF3358 233 VHERHIMPEELDGFEQCWLTGTAAEVTPVGQIGPHSF---EVGELTQDIAKAYEELVR 287
                                        ******************************9988765...799***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (288 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.45
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources