GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__Korea:Ga0059261_3686
          Length = 295

 Score =  281 bits (719), Expect = 1e-80
 Identities = 152/293 (51%), Positives = 186/293 (63%), Gaps = 4/293 (1%)

Query: 1   MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60
           M  + F+GLGNMGG MAANL KAGH V  FDL   A+      G    +SA    EGAE 
Sbjct: 1   MARVGFIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAEGAEA 60

Query: 61  VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120
           VI+MLPAG+HVE +Y  +D +        +LIDCSTI   TAR+VA+AA AKGL  +DAP
Sbjct: 61  VITMLPAGKHVEQVY--EDSVFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAP 118

Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180
           VSGG+  A  GTL+F+VGG A  F RA   L  MG+ + HAG +GAGQ +KICNNMLLG 
Sbjct: 119 VSGGIAAAAGGTLTFMVGGDAAAFERAEVFLAAMGKAVIHAGGNGAGQASKICNNMLLGA 178

Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQ 240
            M  T EAL L  K GLDP    ++   SSG  W+LN Y P PG+ PQ PA NGY GGF 
Sbjct: 179 TMVATCEALLLAQKLGLDPQTFYDIASVSSGACWSLNTYAPLPGMGPQTPADNGYQGGFA 238

Query: 241 VRLMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSIQKL 293
             LM KDL LA+  A++  + TP+GA A  L++    ADA + G+DFS I K+
Sbjct: 239 AGLMLKDLKLAMEAAESTHSETPMGARAAELYTKF--ADAGNAGVDFSGIIKM 289


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: 311
Number of extensions: 12
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: 298
Length of database: 295
Length adjustment: 26
Effective length of query: 272
Effective length of database: 269
Effective search space:    73168
Effective search space used:    73168
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 Ga0059261_3686 Ga0059261_3686 (3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))
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.5991.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-126  404.9  16.4   1.1e-125  404.8  16.4    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3686  Ga0059261_3686 3-hydroxyisobutyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3686  Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.8  16.4  1.1e-125  1.1e-125       1     287 [.       6     290 ..       6     291 .. 0.99

  Alignments for each domain:
  == domain 1  score: 404.8 bits;  conditional E-value: 1.1e-125
                                 TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 
                                               fiGlGnmGg+maanl+kagh vr+fdlsa+a+e++++aG+   +saa+a+e+a++vitmlPagkhve+v
  lcl|FitnessBrowser__Korea:Ga0059261_3686   6 FIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAEGAEAVITMLPAGKHVEQV 74 
                                               9******************************************************************** PP

                                 TIGR01692  70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138
                                               y  ++ +   +  +++lid+stidv +ar+va++a+akG+  +daPvsGG+++a+ GtltfmvGg a++
  lcl|FitnessBrowser__Korea:Ga0059261_3686  75 Y--EDSVFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAPVSGGIAAAAGGTLTFMVGGDAAA 141
                                               *..59**************************************************************** PP

                                 TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207
                                               f+rae  l+amgk ++haG++GaGqa+kiCnn+llg +m+ ++eal l++klGldp+++ +i+s ssG 
  lcl|FitnessBrowser__Korea:Ga0059261_3686 142 FERAEVFLAAMGKAVIHAGGNGAGQASKICNNMLLGATMVATCEALLLAQKLGLDPQTFYDIASVSSGA 210
                                               ********************************************************************* PP

                                 TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276
                                               cWsl+ty+P+PG+ +q+Pa+ngy+gGfa+ lmlkdl+la eaa+s+++++++Ga a ely+ fa++g  
  lcl|FitnessBrowser__Korea:Ga0059261_3686 211 CWSLNTYAPLPGMGPQTPADNGYQGGFAAGLMLKDLKLAMEAAESTHSETPMGARAAELYTKFADAGNA 279
                                               ********************************************************************* PP

                                 TIGR01692 277 kkdfsavikll 287
                                               + dfs++ik+l
  lcl|FitnessBrowser__Korea:Ga0059261_3686 280 GVDFSGIIKML 290
                                               ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (295 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: 7.74
//
[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:

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