Alignments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_0573 N515DRAFT_0573 branched-chain amino acid aminotransferase

Query= reanno::Dyella79:N515DRAFT_2015
         (305 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0573
          Length = 313

 Score =  383 bits (984), Expect = e-111
 Identities = 185/300 (61%), Positives = 234/300 (78%), Gaps = 3/300 (1%)

Query: 8   WIWQNGQIKPWREATTHVMSHALHYGSSVFEGIRSYATPDGAAIFRLTDHLKRLYQSAKI 67
           ++W NGQIKPW EAT HV +HALHYGSSVFEG R YATP G A FRL DH +RL++SA++
Sbjct: 5   FLWHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPAYFRLADHTRRLFESARV 64

Query: 68  YDMVLPYSQDQIAAACRDVIKQNGLGAAYLRPVAYRGLGGFGLSAE--TPIDVAVAAWPM 125
           Y++ + YS+D+I AAC +VI+ N +G+AY+RP+ +RG GG G+ A+   P+DVA+ A   
Sbjct: 65  YEIEVGYSEDEINAACMEVIRANRMGSAYVRPIVFRGAGGLGVLAKPGAPVDVAIMAMEW 124

Query: 126 GPYLGPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGEGIALA 185
           G YLG +A E G D CVSSWQR APNT+P+ AKAGGNYLS QLI  EARR G+ EGIAL 
Sbjct: 125 GAYLG-DAREQGADVCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAEGIALG 183

Query: 186 NTGLLSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDIPREYL 245
           + GLLSEGAGEN+F+V +G L T P SA IL GITR T++TLA + GI+V ERD+PRE L
Sbjct: 184 HNGLLSEGAGENVFVVKNGKLLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDLPREAL 243

Query: 246 YLCDELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWGWLEPV 305
           Y  DE+ M GTAAEITP+RSVD K +G+G+ G +TR +Q+ FFGLF+G+T+D+WGWL PV
Sbjct: 244 YTADEVFMTGTAAEITPVRSVDRKPVGTGRPGPITRALQDAFFGLFDGRTDDRWGWLAPV 303


Lambda     K      H
   0.320    0.138    0.425 

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: 353
Number of extensions: 13
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: 305
Length of database: 313
Length adjustment: 27
Effective length of query: 278
Effective length of database: 286
Effective search space:    79508
Effective search space used:    79508
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 N515DRAFT_0573 N515DRAFT_0573 (branched-chain amino acid aminotransferase)
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.22643.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.7e-125  403.0   0.0   4.2e-125  402.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573  N515DRAFT_0573 branched-chain am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0573  N515DRAFT_0573 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.8   0.0  4.2e-125  4.2e-125       1     298 []       7     303 ..       7     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 4.2e-125
                                    TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipys 66 
                                                  w +G++ ++ +a+vhv thalhYG++vfeG R+Y t++g+a frl +h+ Rl++sa+++++e+ ys
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573   7 WHNGQIKPWTEATVHVSTHALHYGSSVFEGERVYATPQGPAYFRLADHTRRLFESARVYEIEVGYS 72 
                                                  99**************************************************************** PP

                                    TIGR01122  67 keelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGik 132
                                                  ++e++ +++ev+r+n + saY+Rp+v++Ga++lg+ +k +++v+v+i+a+ewgaylg+ a e+G +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573  73 EDEINAACMEVIRANRMGSAYVRPIVFRGAGGLGVLAKPGAPVDVAIMAMEWGAYLGD-AREQGAD 137
                                                  *********************************************************6.9****** PP

                                    TIGR01122 133 vkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgv 198
                                                  v vss++r a+n++p+ aka+gnYl+s+l++ ea+r Gy e+i+L ++G ++eG+Gen+f+vk+g+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 138 VCVSSWQRPAPNTVPSWAKAGGNYLSSQLIGLEARRGGYAEGIALGHNGLLSEGAGENVFVVKNGK 203
                                                  ****************************************************************** PP

                                    TIGR01122 199 lltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrki 264
                                                  lltPp+s  iL gitrd+v++la++lgi+v+e+ + re+lytaDevf+tGtaae+tP+r+vD + +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 204 LLTPPTSAGILAGITRDTVMTLAEDLGIKVEERDLPREALYTADEVFMTGTAAEITPVRSVDRKPV 269
                                                  ****************************************************************** PP

                                    TIGR01122 265 gegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                                  g g+ Gp+t+ lq+aff l+ g+t+++++wl +v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0573 270 GTGRPGPITRALQDAFFGLFDGRTDDRWGWLAPV 303
                                                  ******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (313 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: 6.67
//
[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
the source code
instructions for running GapMind on your computer

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