Alignments for a candidate for mmsB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Shewanella amazonensis SB2B

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate 6937210 Sama_1380 3-hydroxyisobutyrate dehydrogenase (RefSeq)

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__SB2B:6937210
          Length = 301

 Score =  339 bits (869), Expect = 5e-98
 Identities = 184/293 (62%), Positives = 211/293 (72%), Gaps = 5/293 (1%)

Query: 1   MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60
           M  IAF+GLGNMGGPMAANLLKAGH V+VFDL P AV  L  QGA   D+A      A+ 
Sbjct: 1   MAKIAFIGLGNMGGPMAANLLKAGHSVSVFDLNPAAVESLKAQGAGRGDTAQAIAADADF 60

Query: 61  VISMLPAGQHVESLYLGDD---GLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLL 117
           V+SMLPAG+HV  LYLG D   GL+  V    LLIDCSTI   +AR VA+AAAAKGL  +
Sbjct: 61  VVSMLPAGKHVRGLYLGTDTAKGLIEVVKAGCLLIDCSTIDAGSARTVADAAAAKGLEFI 120

Query: 118 DAPVSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNML 177
           DAPVSGG  GA AGTL+FI GG    F +AR VL NMG NIFHAG  GAGQVAKICNNML
Sbjct: 121 DAPVSGGTAGAAAGTLTFICGGTDAAFEKARTVLANMGVNIFHAGGPGAGQVAKICNNML 180

Query: 178 LGILMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAG 237
           L +LM GT+EAL+LG+ +GLDP VLS++MK SSGGNW L  YNP PGVM   P+S GY G
Sbjct: 181 LSVLMVGTSEALSLGIDHGLDPKVLSDIMKVSSGGNWTLEKYNPCPGVMENVPSSKGYQG 240

Query: 238 GFQVRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSI 290
           GF V LM KDLGL+   A   Q+STP+GALAR+L+  HA+A   +   DFSSI
Sbjct: 241 GFMVDLMVKDLGLSQEAALGSQSSTPMGALARSLYVSHARAG--NGTRDFSSI 291


Lambda     K      H
   0.317    0.135    0.395 

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: 375
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: 298
Length of database: 301
Length adjustment: 27
Effective length of query: 271
Effective length of database: 274
Effective search space:    74254
Effective search space used:    74254
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 6937210 Sama_1380 (3-hydroxyisobutyrate dehydrogenase (RefSeq))
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.4981.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-126  407.5  10.1   1.9e-126  407.3  10.1    1.0  1  lcl|FitnessBrowser__SB2B:6937210  Sama_1380 3-hydroxyisobutyrate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937210  Sama_1380 3-hydroxyisobutyrate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.3  10.1  1.9e-126  1.9e-126       1     286 [.       6     294 ..       6     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 407.3 bits;  conditional E-value: 1.9e-126
                         TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvyagde... 74 
                                       fiGlGnmGgpmaanllkagh+v+vfdl+++ave+l+++Ga   ++a++++++ad v++mlPagkhv+ +y+g +   
  lcl|FitnessBrowser__SB2B:6937210   6 FIGLGNMGGPMAANLLKAGHSVSVFDLNPAAVESLKAQGAGRGDTAQAIAADADFVVSMLPAGKHVRGLYLGTDtak 82 
                                       9*********************************************************************9865333 PP

                         TIGR01692  75 gilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefaraepvleamgk 151
                                       g+++ vk + llid+stid+ sar+va++aaakG+ f+daPvsGG++ga+aGtltf+ Gg++++f++a+ vl++mg 
  lcl|FitnessBrowser__SB2B:6937210  83 GLIEVVKAGCLLIDCSTIDAGSARTVADAAAAKGLEFIDAPVSGGTAGAAAGTLTFICGGTDAAFEKARTVLANMGV 159
                                       899************************************************************************** PP

                         TIGR01692 152 nivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWsldtynPvPGvveqaPasn 228
                                       ni+haG+ GaGq+akiCnn+ll++ m+G++eal+lg+  Gldpkvl++i++ ssG +W+l+ ynP PGv+e++P+s+
  lcl|FitnessBrowser__SB2B:6937210 160 NIFHAGGPGAGQVAKICNNMLLSVLMVGTSEALSLGIDHGLDPKVLSDIMKVSSGGNWTLEKYNPCPGVMENVPSSK 236
                                       ***************************************************************************** PP

                         TIGR01692 229 gykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdfsavikl 286
                                       gy+gGf ++lm+kdlgl+qeaa   ++s+++Galar ly  +a +g g +dfs++++ 
  lcl|FitnessBrowser__SB2B:6937210 237 GYQGGFMVDLMVKDLGLSQEAALGSQSSTPMGALARSLYVSHARAGNGTRDFSSIFEH 294
                                       *******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (301 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: 00:00:00.00
# Mc/sec: 9.92
//
[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