GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Sinorhizobium meliloti 1021

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate SMc01214 SMc01214 zinc-containing alcohol dehydrogenase

Query= BRENDA::Q6ECH5
         (336 letters)



>FitnessBrowser__Smeli:SMc01214
          Length = 347

 Score =  190 bits (482), Expect = 5e-53
 Identities = 103/328 (31%), Positives = 166/328 (50%), Gaps = 13/328 (3%)

Query: 1   MEALVLTGKKQLEIEDIKEPEIKPDEVLIHTAYAGICGTDKALYAGLPGSASAVPPIVLG 60
           M+A+ L     + + ++  PE  PD++L+     GICGTD+ L   L G   + PP+ LG
Sbjct: 1   MKAVRLESVGNISVRNVGIPEPGPDDLLVKVEACGICGTDRHL---LHGEFPSTPPVTLG 57

Query: 61  HENSGVVTKVGSEVTNVKPGDRVTVDPNIYCGQCKYCRTQRPELCEHLDAVGVTRNGGFE 120
           HE  G+V + GS V ++ PG R+T DPNI CG+C  C+  R  LC +L A+G+ R+GGF 
Sbjct: 58  HEFCGIVVEAGSAVRDIAPGARITGDPNISCGRCPQCQAGRVNLCRNLRAIGIHRDGGFA 117

Query: 121 EYFTAPAKVVYPIPDDVSLKAAAVVEPISCAMHGVDLLETHPYQKALVLGDGFEGQLFAQ 180
           EY   P K  + IP  +     A  EP++C +HGVDL          +LG G  G L  Q
Sbjct: 118 EYVLVPRKQAFEIPLTLDPVHGAFCEPLACCLHGVDLSGIKAGSTVAILGGGVIGLLTVQ 177

Query: 181 ILKARGIHEVTLAGRSDEKLENNRKHFGVKTIDTTKEEI----------PADAYDIVVEA 230
           + +  G   V L+ R   K     +     T+D +  ++               D+V+E 
Sbjct: 178 LARLAGATTVILSTRQATKRRLAEEVGATATVDPSAGDVVEAIAGPVGLVPGGVDVVIEC 237

Query: 231 VGLPATQEQALAAAARGAQVLMFGVGNPDDKFSVNTYDVFQKQLTIQGAFVNPYTFEDSI 290
            G+  T +Q+   A  G  V++ GV    +K  +  +D+  ++L + G+F+NP+    + 
Sbjct: 238 AGVAETVKQSTRLAKAGGTVVILGVLPQGEKVEIEPFDILFRELRVLGSFINPFVHRRAA 297

Query: 291 ALLSSGVVDPLPLFSHELDLDGVEDFVS 318
            L+++G ++   + S  + LD   D +S
Sbjct: 298 DLVATGAIEIDRMISRRISLDEAPDVIS 325


Lambda     K      H
   0.316    0.136    0.393 

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: 289
Number of extensions: 17
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: 336
Length of database: 347
Length adjustment: 29
Effective length of query: 307
Effective length of database: 318
Effective search space:    97626
Effective search space used:    97626
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.

Links

Downloads

Related tools

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