GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Sinorhizobium meliloti 1021

Align Lmo2664 protein (characterized, see rationale)
to candidate SM_b20853 SM_b20853 sugar-alcohol dehydrogenase

Query= uniprot:Q8Y413
         (350 letters)



>FitnessBrowser__Smeli:SM_b20853
          Length = 339

 Score =  200 bits (509), Expect = 4e-56
 Identities = 117/350 (33%), Positives = 184/350 (52%), Gaps = 16/350 (4%)

Query: 1   MRAAVLYENNVIKAEQIDEATCGKDQVRVEVKAVGICGSDIHKMQTRWKYPLPAVMGHEF 60
           MRA VL+    I+ E   +   G  +V + V +VG+CGSD+ +M  +  + +P + GHEF
Sbjct: 1   MRAIVLHAPGDIRLETRPKPVAGPGEVLLRVASVGVCGSDLPRMLVKGAWKMPLITGHEF 60

Query: 61  AGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGSHFHGGFAENV 120
           +G I  +G  V    +G+  A  PL PC +C  CK G+F+ C +Y   GS   G +AE V
Sbjct: 61  SGHIHALGENVEGWEIGELTAIAPLMPCNQCIECKTGNFSRCRDYDYFGSRRDGAYAEFV 120

Query: 121 VMKADNVISIGD-LDFEEGAMIEPLAVSMHGVL---GIQPRLGDTVIVFGIGTIGILVVQ 176
            +  +N+I     +D    AM +P ++++H +    GI    G T  V G G IG+  +Q
Sbjct: 121 AVPVENLIKTPQHVDPRAIAMTDPASIALHAIWKAGGI--TAGQTGAVVGCGPIGLFAIQ 178

Query: 177 CLLLAGVKDIIAVDISDKKLADAREFGCKYTI-NPKNEDLKERVFAYTNGLGADIALECA 235
            + + G   +IAVD++++KLA AR+ G    I +    D KER         AD+ +E  
Sbjct: 179 WMRIMGTSRVIAVDVTEEKLALARQAGADLCILSADFADNKER---------ADLVIEAV 229

Query: 236 GSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWNSYSAPFPGE 295
           G   T    +++    G V F+GI   DV L    F+   R+E++L G WNS+ APFPG 
Sbjct: 230 GIDSTINAAVMLAAPGGHVTFIGIPVPDVKLSNATFQRFLRQEVSLHGSWNSFGAPFPGP 289

Query: 296 EWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSREHDYNKVMILP 345
           +W T+++    G +K + +ISH   L E    F    +++  ++KV+  P
Sbjct: 290 QWTTTVQKFATGELKWEFMISHDLDLAELPGIFQRFAAKDLHFSKVLFRP 339


Lambda     K      H
   0.321    0.139    0.417 

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: 302
Number of extensions: 15
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: 350
Length of database: 339
Length adjustment: 29
Effective length of query: 321
Effective length of database: 310
Effective search space:    99510
Effective search space used:    99510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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