Alignments for a candidate for ilvE in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Phyllobacterium brassicacearum STM 196

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_106710446.1 CU102_RS07375 branched-chain amino acid aminotransferase

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



>NCBI__GCF_003010955.1:WP_106710446.1
          Length = 296

 Score =  224 bits (571), Expect = 2e-63
 Identities = 117/262 (44%), Positives = 164/262 (62%), Gaps = 5/262 (1%)

Query: 7   DGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNS 66
           +G IWM+G+ + W DAK+HVLTH LHY   VFEG RAY     G  IF+L EHT+RL  S
Sbjct: 10  EGYIWMNGEFVRWADAKVHVLTHGLHYASSVFEGERAY-----GGEIFKLNEHTERLHES 64

Query: 67  AKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIAAW 126
           AKI    +PF  E L  A  +++ +   ++ Y+RPI W GSE +GVSA+ N I+VAIA W
Sbjct: 65  AKILGFKIPFTVEELNDACRKLLAKQGFQNAYVRPIAWRGSESMGVSAQANKINVAIAIW 124

Query: 127 PWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALL 186
            W +Y       KGIR+  + + R     +  ++KA+G Y+   ++   A A GY +AL+
Sbjct: 125 QWPSYFDPAQKLKGIRLDLAEYRRPDPRTAPSKSKAAGLYMICTISKHAAEAKGYADALM 184

Query: 187 LDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDE 246
           LD  G V+E +G N F V +G ++TP     LDGITR TVI LA+  G +V+E+ I  +E
Sbjct: 185 LDWRGQVAEATGANVFFVKDGVIHTPTPDCFLDGITRRTVIDLAKRRGYEVVERAIMPEE 244

Query: 247 VYTCDEAFFTGTAAEVTPIREL 268
           + + ++ F TGTAAEVTP+ E+
Sbjct: 245 LDSFEQCFLTGTAAEVTPVSEI 266


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: 250
Number of extensions: 8
Number of successful extensions: 2
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: 296
Length adjustment: 27
Effective length of query: 280
Effective length of database: 269
Effective search space:    75320
Effective search space used:    75320
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 WP_106710446.1 CU102_RS07375 (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.2392360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-90  289.5   0.0    1.6e-90  289.3   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106710446.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106710446.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.3   0.0   1.6e-90   1.6e-90       1     281 [.      14     285 ..      14     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 289.3 bits;  conditional E-value: 1.6e-90
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w++Ge+v+++dakvhvlth+lhY ++vfeG RaY +     if+l+eh+eRl++sakil ++ip++ eel+++
  NCBI__GCF_003010955.1:WP_106710446.1  14 WMNGEFVRWADAKVHVLTHGLHYASSVFEGERAYGG----EIFKLNEHTERLHESAKILGFKIPFTVEELNDA 82 
                                           9*********************************99....9******************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           ++++l k+++++aY+Rp++++G+e++g++++++ k++v+ia w+w+ y++     kGi+  ++ +rr ++ + 
  NCBI__GCF_003010955.1:WP_106710446.1  83 CRKLLAKQGFQNAYVRPIAWRGSESMGVSAQAN-KINVAIAIWQWPSYFDPAQKLKGIRLDLAEYRRPDPRTA 154
                                           ******************************777.*****************9999****************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p+k kaag Y+  ++ k+ a ++Gy +a++Ld  G vae +G n+f vkdgv+ tP   +  L+gitr +vi+
  NCBI__GCF_003010955.1:WP_106710446.1 155 PSKSKAAGLYMICTISKHAAEAKGYADALMLDWRGQVAEATGANVFFVKDGVIHTPTP-DCFLDGITRRTVID 226
                                           *********************************************************9.99************ PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaff 281
                                           lak++g+ev+e+ i  eel   +  fltGtaaevtP+ e+   +    ++G++  +l++ + 
  NCBI__GCF_003010955.1:WP_106710446.1 227 LAKRRGYEVVERAIMPEELDSFEQCFLTGTAAEVTPVSEIGPHRF---TVGEIAINLMNDYA 285
                                           ***************************************987765...46667777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (296 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: 26.03
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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