Alignments for a candidate for mmsB in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Caulobacter crescentus NA1000

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate CCNA_01416 CCNA_01416 3-hydroxyisobutyrate dehydrogenase

Query= reanno::psRCH2:GFF2390
         (296 letters)



>FitnessBrowser__Caulo:CCNA_01416
          Length = 298

 Score =  262 bits (670), Expect = 6e-75
 Identities = 149/291 (51%), Positives = 177/291 (60%), Gaps = 3/291 (1%)

Query: 3   IGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAELII 62
           I FIGLGNMG  MA N  KA HQ+  FDL+AAAVE  V AG L   S  A A   AE++I
Sbjct: 4   IAFIGLGNMGGGMAANQAKAQHQVRAFDLSAAAVERAVAAGCLAAAS-VAEAVAEAEIVI 62

Query: 63  TMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAPVS 122
           TMLPA  HV+ VY     ++ ++    +LIDCSTID  SAR VA+ AAE G    DAPVS
Sbjct: 63  TMLPAGPHVRAVY--AEQILPNAPKSALLIDCSTIDVDSARVVARQAAEAGFRFADAPVS 120

Query: 123 GGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGISM 182
           GG   A AGTL FMVG    DF   +  LA M +  +H G  G GQ AK+ NNMLLG+SM
Sbjct: 121 GGIMAAEAGTLAFMVGCEASDFAAVEAALAPMSRVTIHAGDHGAGQAAKICNNMLLGVSM 180

Query: 183 IGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFGSD 242
           +G  EA AL   LG+ A     + + SSG+CWS  +Y P PGV    P+ RGY GGF S 
Sbjct: 181 LGTCEAFALAEKLGLAADRFFEIASKSSGQCWSITSYCPVPGVGPQTPADRGYEGGFASA 240

Query: 243 LMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAIINQYR 293
           +MLKDL LA EAA +      +GA A+ LY  F A G GG DFSA+I   R
Sbjct: 241 MMLKDLKLAQEAAAKAGASTPMGAQAEALYALFDANGFGGKDFSAVIELLR 291


Lambda     K      H
   0.318    0.134    0.392 

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: 270
Number of extensions: 9
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: 296
Length of database: 298
Length adjustment: 26
Effective length of query: 270
Effective length of database: 272
Effective search space:    73440
Effective search space used:    73440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate CCNA_01416 CCNA_01416 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

# 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/TIGR01692.hmm
# target sequence database:        /tmp/gapView.14215.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01692  [M=288]
Accession:   TIGR01692
Description: HIBADH: 3-hydroxyisobutyrate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-147  476.5  12.8   1.7e-147  476.3  12.8    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01416  CCNA_01416 3-hydroxyisobutyrate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01416  CCNA_01416 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.3  12.8  1.7e-147  1.7e-147       1     288 []       6     291 ..       6     291 .. 1.00

  Alignments for each domain:
  == domain 1  score: 476.3 bits;  conditional E-value: 1.7e-147
                             TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagd 73 
                                           fiGlGnmGg+maan++ka+h+vr+fdlsa+ave++v+aG+ aaas+aeav+ea++vitmlPag hv++vya  
  lcl|FitnessBrowser__Caulo:CCNA_01416   6 FIGLGNMGGGMAANQAKAQHQVRAFDLSAAAVERAVAAGCLAAASVAEAVAEAEIVITMLPAGPHVRAVYA-- 76 
                                           9*********************************************************************6.. PP

                             TIGR01692  74 egilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvl 146
                                           e+il+++ k++llid+stidvdsar+va++aa++G++f+daPvsGG+++a+aGtl+fmvG+ea++fa++e++l
  lcl|FitnessBrowser__Caulo:CCNA_01416  77 EQILPNAPKSALLIDCSTIDVDSARVVARQAAEAGFRFADAPVSGGIMAAEAGTLAFMVGCEASDFAAVEAAL 149
                                           ************************************************************************* PP

                             TIGR01692 147 eamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPG 219
                                           ++m+++++haGd+GaGqaakiCnn+llg+sm+G++ea+al+eklGl++++++ei+skssG+cWs+++y+PvPG
  lcl|FitnessBrowser__Caulo:CCNA_01416 150 APMSRVTIHAGDHGAGQAAKICNNMLLGVSMLGTCEAFALAEKLGLAADRFFEIASKSSGQCWSITSYCPVPG 222
                                           ************************************************************************* PP

                             TIGR01692 220 vveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavikllr 288
                                           v +q+Pa++gy+gGfa+a+mlkdl+laqeaa++++as+++Ga+a++ly+lf+++g+g+kdfsavi+llr
  lcl|FitnessBrowser__Caulo:CCNA_01416 223 VGPQTPADRGYEGGFASAMMLKDLKLAQEAAAKAGASTPMGAQAEALYALFDANGFGGKDFSAVIELLR 291
                                           *******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (298 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.13
//
[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