Aligments for a candidate for ilvE in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for ilvE in Desulfovibrio vulgaris Hildenborough

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate 208718 DVU3197 branched-chain amino acid aminotransferase

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



>MicrobesOnline__882:208718
          Length = 309

 Score =  369 bits (946), Expect = e-107
 Identities = 172/304 (56%), Positives = 224/304 (73%)

Query: 1   MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60
           MSM  +   IW DGK + W +A +HVLTH LHYG+GVFEG+RAY+ ADG +A+FRL+EH 
Sbjct: 1   MSMVQKSETIWFDGKQVPWDEANVHVLTHALHYGVGVFEGIRAYRCADGSSAVFRLREHV 60

Query: 61  KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120
           +RL +SAKI +M++PF  + +  A  E ++ N+L   Y+RP+ +VG+  +GV    N + 
Sbjct: 61  QRLFSSAKILRMEIPFTEDAIFDAIVETLQRNRLAEGYIRPLSFVGAGAMGVYPGDNPVQ 120

Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180
             IA WPWGAYLG + + KGIRVKTSSF RHHVN  M +AKASG YVNS+LA  EA ADG
Sbjct: 121 TIIAVWPWGAYLGAEALEKGIRVKTSSFARHHVNAMMTKAKASGNYVNSVLAKMEAKADG 180

Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240
           YDEAL+LDV G+VSE +GEN F+V NG + T  L+S LDGITR++++TLARD G +V+E+
Sbjct: 181 YDEALMLDVSGFVSEATGENIFMVRNGVIKTTPLTSILDGITRNSLMTLARDLGYEVVEQ 240

Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300
           + TRDE+Y  DEAFF GTAAEVTPIRE+D R IG G+ GP+T+ LQ  +F  V G +  Y
Sbjct: 241 QFTRDELYVADEAFFCGTAAEVTPIREVDRRVIGKGSAGPVTKHLQQEYFKAVKGDNPSY 300

Query: 301 ANWL 304
            +WL
Sbjct: 301 DHWL 304


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: 348
Number of extensions: 6
Number of successful extensions: 1
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: 309
Length adjustment: 27
Effective length of query: 280
Effective length of database: 282
Effective search space:    78960
Effective search space used:    78960
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 208718 DVU3197 (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.4171.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-136  440.6   0.0   1.4e-136  440.4   0.0    1.0  1  lcl|MicrobesOnline__882:208718  DVU3197 branched-chain amino aci


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208718  DVU3197 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.4   0.0  1.4e-136  1.4e-136       1     296 [.      11     305 ..      11     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 440.4 bits;  conditional E-value: 1.4e-136
                       TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskeelvevtkevl 78 
                                     w+dG+ v++++a+vhvlthalhYG gvfeGiRaY+  +  +a+frl+ehv+Rl+ sakilr+eip++++ + ++++e+l
  lcl|MicrobesOnline__882:208718  11 WFDGKQVPWDEANVHVLTHALHYGVGVFEGIRAYRCADgSSAVFRLREHVQRLFSSAKILRMEIPFTEDAIFDAIVETL 89 
                                     9**********************************9883579************************************* PP

                       TIGR01122  79 rknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnYl 157
                                     ++n l + YiRpl +vGa+ +g++p  d +v+ iia+w+wgaylg+ealekGi+vk+ssf+r++vn+++tkaka+gnY+
  lcl|MicrobesOnline__882:208718  90 QRNRLAEGYIRPLSFVGAGAMGVYP-GDNPVQTIIAVWPWGAYLGAEALEKGIRVKTSSFARHHVNAMMTKAKASGNYV 167
                                     *************************.999************************************************** PP

                       TIGR01122 158 nsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeerisre 236
                                     ns+lak+ea++ Gydea++Ld +G+v+e +Genif+v++gv++t p+ +siL+gitr+++++la++lg+ev+e++++r+
  lcl|MicrobesOnline__882:208718 168 NSVLAKMEAKADGYDEALMLDVSGFVSEATGENIFMVRNGVIKTTPL-TSILDGITRNSLMTLARDLGYEVVEQQFTRD 245
                                     **********************************************9.78***************************** PP

                       TIGR01122 237 elytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlt 296
                                     ely+aDe+f+ GtaaevtPirevD r ig+g++Gpvtk+lq+++f+ v+g+++++++wl+
  lcl|MicrobesOnline__882:208718 246 ELYVADEAFFCGTAAEVTPIREVDRRVIGKGSAGPVTKHLQQEYFKAVKGDNPSYDHWLH 305
                                     **********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (309 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.85
//
[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, or view the source code.

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