GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Herbaspirillum seropedicae SmR1

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase

Query= BRENDA::Q8KQG6
         (338 letters)



>FitnessBrowser__HerbieS:HSERO_RS04830
          Length = 341

 Score =  126 bits (316), Expect = 9e-34
 Identities = 95/311 (30%), Positives = 148/311 (47%), Gaps = 23/311 (7%)

Query: 3   ALVLTGTKKLEVKDIDRPKVLPNEVLIHTAFAGICGTD-HALYAGLPGSADAVPPIVLGH 61
           A+V    K L ++ +  P   P ++L+    +G+C TD HA +   P      PP + GH
Sbjct: 8   AVVREFGKPLSIEQVPVPTPAPGQILVKFEASGVCHTDLHAAHGDWP--VKPTPPFIPGH 65

Query: 62  ENSGVVAEIGSAVTNVKVGDRVTVD-PNIYCGQCKYCRTARPELCENLSAVGVTRDGGFE 120
           E +G VA +G+ V +VK GDRV V   +  CG C  CRT    LC      G + +G F 
Sbjct: 66  EGTGYVAAVGAGVKHVKEGDRVGVPWLHTACGCCSPCRTGWETLCAEQQNTGYSVNGSFA 125

Query: 121 EFFTAPASVVYPIPDNVSLKSAAVVEPISCA----VHGIQLLKVTPYQKALVIGDGFMGE 176
           E+  A    V  +PDN+    AA   P+ CA      G++  +V P +  ++ G G +G 
Sbjct: 126 EYGLADPKFVGHLPDNLDFGPAA---PVLCAGVTVYKGLKETEVRPGEWVVISGIGGLGH 182

Query: 177 LFVQILQAYGIHQVDLAGIVDEKLAMNKEKFGVKNTYNTMKGDKIPE------GEYDVII 230
           + VQ  +A G+H V  A I ++KLA+ K K G   T +    + + E      G +  ++
Sbjct: 183 MAVQYAKAMGMHVV-AADIHEDKLALAK-KLGADLTVDGRNHNAVAEVQRIIGGAHGALV 240

Query: 231 EAVGLPQTQEAAIEASARGAQVLMFGVGGPDAKFQMNTYEVFQKQLTIQGSFINPNA-FE 289
            AV     ++A     ARG   L   VG P     +  +    K++T++GS +      E
Sbjct: 241 TAVSPKAMEQAFGFLRARGTMAL---VGLPPGDISLPVFNTVLKRITVRGSIVGTRQDLE 297

Query: 290 DSLALLSSGKL 300
           +SL   + GK+
Sbjct: 298 ESLVFAAEGKV 308


Lambda     K      H
   0.317    0.136    0.390 

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: 264
Number of extensions: 20
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: 338
Length of database: 341
Length adjustment: 28
Effective length of query: 310
Effective length of database: 313
Effective search space:    97030
Effective search space used:    97030
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 (21.6 bits)
S2: 49 (23.5 bits)

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