GapMind for Amino acid biosynthesis

 

Alignments 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.aa/TIGR01122.hmm
# target sequence database:        /tmp/gapView.8697.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.90
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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