Alignments for a candidate for ilvE in Thermovibrio ammonificans HB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Thermovibrio ammonificans HB-1

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013537848.1 THEAM_RS05500 branched-chain amino acid transaminase

Query= BRENDA::F0QW25
         (314 letters)



>NCBI__GCF_000185805.1:WP_013537848.1
          Length = 304

 Score =  296 bits (757), Expect = 5e-85
 Identities = 147/302 (48%), Positives = 205/302 (67%), Gaps = 2/302 (0%)

Query: 15  KYVWVNGKLIPEKEATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHDS 74
           ++ +  GK +P +EA I I T++ HYGT++FEGIRAYWN +   L+    ++HY R   +
Sbjct: 3   RFAYFEGKFVPVEEANINIQTNSFHYGTAVFEGIRAYWNEEKKQLFGLFVKEHYERMLAN 62

Query: 75  AKIMSIKVGYSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAIIT 134
            KI+++KV  S  EL + TVELLR     ED YIRPI + +   ++  +       AI T
Sbjct: 63  CKILNLKVEKSAQELTEITVELLRRCGHREDTYIRPIAYFADLKISPKLIGYKTELAIYT 122

Query: 135 VPFGHYLE-PKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLN 193
           VP G YL+  +G+KAK  SW R++++M P + KV+G YVNS  A  +A ++G+DEAI+LN
Sbjct: 123 VPLGDYLDLSRGLKAKTASWHRINDTMIPARCKVAGAYVNSAFAKTEALLNGYDEAIMLN 182

Query: 194 RDGYVAEGSGENIFIIKDGILYTPPVYDSILEGITRDTVITIAR-DLGLTVTEKRITREE 252
            DG VAEGSGEN+FI+++G L T P   +ILEGITR+ VI +AR +LG+ V E+ I R E
Sbjct: 183 PDGTVAEGSGENVFIVRNGKLITTPSASNILEGITRNAVIHLAREELGIEVEERPILRSE 242

Query: 253 LYTADEVFFTGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVHGRVSKYKNWLTP 312
           LY ADEVF+TGTAA+V PVV +D  VIGNGE GP+  +++  Y  +V G   KY++WLTP
Sbjct: 243 LYVADEVFYTGTAAQVAPVVQVDHVVIGNGEVGPVTKRLQEIYFSIVKGNNPKYEHWLTP 302

Query: 313 IY 314
           +Y
Sbjct: 303 VY 304


Lambda     K      H
   0.321    0.139    0.409 

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: 319
Number of extensions: 18
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: 314
Length of database: 304
Length adjustment: 27
Effective length of query: 287
Effective length of database: 277
Effective search space:    79499
Effective search space used:    79499
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_013537848.1 THEAM_RS05500 (branched-chain amino acid transaminase)
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.22252.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-114  366.8   0.1   4.4e-114  366.6   0.1    1.0  1  lcl|NCBI__GCF_000185805.1:WP_013537848.1  THEAM_RS05500 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013537848.1  THEAM_RS05500 branched-chain amino acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.6   0.1  4.4e-114  4.4e-114       1     298 []       6     303 ..       6     303 .. 0.97

  Alignments for each domain:
  == domain 1  score: 366.6 bits;  conditional E-value: 4.4e-114
                                 TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaif..rlkehveRlydsakilrleipysk 67 
                                               +++G++v+ve+a++++ t+++hYGt+vfeGiRaY++++++++f  ++keh+eR++ + kil+l+++ s+
  lcl|NCBI__GCF_000185805.1:WP_013537848.1   6 YFEGKFVPVEEANINIQTNSFHYGTAVFEGIRAYWNEEKKQLFglFVKEHYERMLANCKILNLKVEKSA 74 
                                               89**********************************99888874478********************** PP

                                 TIGR01122  68 eelvevtkevlrknnlks.aYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvk 134
                                               +el+e+t+e+lr+ + ++ +YiRp++y  + dl+++pk +++k+e++i+++++g yl+   l++G+k+k
  lcl|NCBI__GCF_000185805.1:WP_013537848.1  75 QELTEITVELLRRCGHREdTYIRPIAY--FADLKISPKlIGYKTELAIYTVPLGDYLD---LSRGLKAK 138
                                               *************998877********..89**************************9...89****** PP

                                 TIGR01122 135 vssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPp 203
                                               ++s++r ++ +ip++ k+ag+Y+ns++ak+eal +Gydeai+L+ +G vaeGsGen+fiv++g+l+t p
  lcl|NCBI__GCF_000185805.1:WP_013537848.1 139 TASWHRINDTMIPARCKVAGAYVNSAFAKTEALLNGYDEAIMLNPDGTVAEGSGENVFIVRNGKLITTP 207
                                               ******************************************************************999 PP

                                 TIGR01122 204 vsesiLkgitrdaviklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGp 271
                                                +++iL+gitr+avi+la+ elgiev+e++i r+ely+aDevf tGtaa v+P+++vD++ ig+g++Gp
  lcl|NCBI__GCF_000185805.1:WP_013537848.1 208 SASNILEGITRNAVIHLAReELGIEVEERPILRSELYVADEVFYTGTAAQVAPVVQVDHVVIGNGEVGP 276
                                               99****************9789*********************************************** PP

                                 TIGR01122 272 vtkklqeaffdlvegktekkeewltyv 298
                                               vtk+lqe +f +v+g+++k+e+wlt+v
  lcl|NCBI__GCF_000185805.1:WP_013537848.1 277 VTKRLQEIYFSIVKGNNPKYEHWLTPV 303
                                               ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (304 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: 7.71
//
[ok]

This GapMind analysis is from Apr 10 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