Alignments for a candidate for ilvE in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Acidovorax sp. GW101-3H11

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Ac3H11_3369 Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Query= reanno::BFirm:BPHYT_RS16285
         (307 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3369
          Length = 305

 Score =  458 bits (1178), Expect = e-134
 Identities = 217/306 (70%), Positives = 260/306 (84%), Gaps = 2/306 (0%)

Query: 3   MADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKR 62
           MADRDGKIWMDG+++DWRDAKIHVLTHTLHYG G FEGVRAY TA+G TAIFRL+EHT R
Sbjct: 1   MADRDGKIWMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTANG-TAIFRLEEHTDR 59

Query: 63  LLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVA 122
           L NSAKI +M +PF  E +  AQ  VVRENKLESCYLRP+ W+GS+KLGVS KGN IH+ 
Sbjct: 60  LFNSAKILRMKIPFTKEEVNEAQKAVVRENKLESCYLRPLTWIGSQKLGVSPKGNQIHLM 119

Query: 123 IAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYD 182
           +AAW WGAYLGE+G+ +GIRVKTSS+TRHHVN++M +AKA   Y NSILAN EA+ DGYD
Sbjct: 120 VAAWAWGAYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYD 179

Query: 183 EALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSS-CLDGITRDTVITLARDAGIQVIEKR 241
           EALLLD  G+VSEG+GEN F++ NG +YTPDLS+  L+GITR+TV  +A+D G+++++KR
Sbjct: 180 EALLLDSSGFVSEGAGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKR 239

Query: 242 ITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYA 301
           ITRDEVY  DEAFFTGTAAEVTPIRELD   +GSG+RGPITEK+QS FFDIVNG++  YA
Sbjct: 240 ITRDEVYIADEAFFTGTAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYA 299

Query: 302 NWLTKI 307
           +WLTK+
Sbjct: 300 HWLTKV 305


Lambda     K      H
   0.319    0.136    0.411 

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: 384
Number of extensions: 4
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: 307
Length of database: 305
Length adjustment: 27
Effective length of query: 280
Effective length of database: 278
Effective search space:    77840
Effective search space used:    77840
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 Ac3H11_3369 (Branched-chain amino acid aminotransferase (EC 2.6.1.42))
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.30148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.6e-141  455.2   0.2   5.1e-141  455.1   0.2    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369  Branched-chain amino acid aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369  Branched-chain amino acid aminotransferase (EC 2.6.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.1   0.2  5.1e-141  5.1e-141       1     298 []       9     305 .]       9     305 .] 0.99

  Alignments for each domain:
  == domain 1  score: 455.1 bits;  conditional E-value: 5.1e-141
                                        TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrle 62 
                                                      w+dG++vd++dak+hvlth+lhYG g feG+RaY+t +g+aifrl+eh++Rl++sakilr++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369   9 WMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTANGTAIFRLEEHTDRLFNSAKILRMK 70 
                                                      9************************************************************* PP

                                        TIGR01122  63 ipyskeelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylge 124
                                                      ip++kee++e++k v+r+n+l+s+Y+Rpl ++G+++lg++pk + ++++++aaw+wgaylge
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369  71 IPFTKEEVNEAQKAVVRENKLESCYLRPLTWIGSQKLGVSPKGN-QIHLMVAAWAWGAYLGE 131
                                                      *****************************************655.9**************** PP

                                        TIGR01122 125 ealekGikvkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeG 186
                                                      e+l++Gi+vk+ss++r++vn+ +t+aka++nY ns+la++eal  Gydea+lLd++G+v+eG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 132 EGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYDEALLLDSSGFVSEG 193
                                                      ************************************************************** PP

                                        TIGR01122 187 sGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltG 248
                                                      +Genif++k+gv++tP++s  +L+gitr++v ++ak+lg+e++++ri+r+e+y+aDe+f+tG
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 194 AGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKRITRDEVYIADEAFFTG 255
                                                      ************************************************************** PP

                                        TIGR01122 249 taaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                                      taaevtPire+D +++g+g+rGp+t+k+q+affd+v+g++ ++++wlt+v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 256 TAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYAHWLTKV 305
                                                      ***********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (305 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: 11.19
//
[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