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.1978569.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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.65
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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