Alignments for a candidate for ilvE in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Caulobacter crescentus NA1000

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate CCNA_03024 CCNA_03024 branched-chain amino acid aminotransferase

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



>FitnessBrowser__Caulo:CCNA_03024
          Length = 296

 Score =  243 bits (621), Expect = 3e-69
 Identities = 123/264 (46%), Positives = 167/264 (63%), Gaps = 5/264 (1%)

Query: 5   DRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLL 64
           DRDG IW+DG+ + WR+AK+HVLTH LHY   VFEG R Y     G  IF+L EHT+RL 
Sbjct: 8   DRDGWIWLDGQFVPWREAKVHVLTHGLHYASSVFEGERMY-----GGEIFKLTEHTERLF 62

Query: 65  NSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIA 124
            SA+I   ++P+    +  A      +N L+ CY+RPI W GSE +GVSA+ + IHVAIA
Sbjct: 63  KSAEILDFEIPYTVAEIDEACKATAAKNGLKDCYVRPIAWRGSEMIGVSAQQSKIHVAIA 122

Query: 125 AWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEA 184
            W W +Y      AKGIR+  + + R     + + AKA+G Y+   ++   A  DGY +A
Sbjct: 123 VWEWPSYFDPATKAKGIRLTWAKYQRPDPKTAPIAAKAAGLYMICTISKHAAEKDGYADA 182

Query: 185 LLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITR 244
           ++LD  GYV+E +G N F V +G L+TP     LDGITR TVI LA+  GI+V+E+ I +
Sbjct: 183 MMLDYRGYVAEATGANVFFVKDGVLHTPKPDCFLDGITRRTVIDLAKAKGIEVVERHIQK 242

Query: 245 DEVYTCDEAFFTGTAAEVTPIREL 268
           +E+ T  E F  GTAAEVTP+ E+
Sbjct: 243 EELATFTECFIVGTAAEVTPVSEV 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: 304
Number of extensions: 11
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 CCNA_03024 CCNA_03024 (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.aa/TIGR01122.hmm
# target sequence database:        /tmp/gapView.11596.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-92  295.1   0.0    2.9e-92  295.0   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03024  CCNA_03024 branched-chain amino 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03024  CCNA_03024 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.0   0.0   2.9e-92   2.9e-92       1     287 [.      14     291 ..      14     296 .] 0.96

  Alignments for each domain:
  == domain 1  score: 295.0 bits;  conditional E-value: 2.9e-92
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           wldG++v++++akvhvlth+lhY ++vfeG R+Y +     if+l+eh+eRl++sa+il++eipy+  e+ e+
  lcl|FitnessBrowser__Caulo:CCNA_03024  14 WLDGQFVPWREAKVHVLTHGLHYASSVFEGERMYGG----EIFKLTEHTERLFKSAEILDFEIPYTVAEIDEA 82 
                                           9*********************************99....9******************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                           +k +  kn+lk++Y+Rp++++G+e +g+++  + k++v+ia+wew+ y++  +  kGi+ + + ++r ++++ 
  lcl|FitnessBrowser__Caulo:CCNA_03024  83 CKATAAKNGLKDCYVRPIAWRGSEMIGVSA-QQSKIHVAIAVWEWPSYFDPATKAKGIRLTWAKYQRPDPKTA 154
                                           ******************************.778*************************************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p +akaag Y+  ++ k+ a + Gy +a++Ld  Gyvae +G n+f vkdgvl tP+  +  L+gitr +vi+
  lcl|FitnessBrowser__Caulo:CCNA_03024 155 PIAAKAAGLYMICTISKHAAEKDGYADAMMLDYRGYVAEATGANVFFVKDGVLHTPKP-DCFLDGITRRTVID 226
                                           *********************************************************9.99************ PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287
                                           lak +giev+e++i +eel t  e f+ GtaaevtP+ ev + k    k   +   l++++  lv+g+
  lcl|FitnessBrowser__Caulo:CCNA_03024 227 LAKAKGIEVVERHIQKEELATFTECFIVGTAAEVTPVSEVGEFKFTPAK---LSLDLMDTYAALVRGE 291
                                           ****************************************999987654...5667777777777776 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: 10.19
//
[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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis