GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Sinorhizobium meliloti 1021

Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate SM_b20854 SM_b20854 sugar uptake ABC transporter permease

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__Smeli:SM_b20854
          Length = 331

 Score =  192 bits (487), Expect = 1e-53
 Identities = 111/303 (36%), Positives = 170/303 (56%), Gaps = 10/303 (3%)

Query: 33  ITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSI-SQIGMVSCTMMFCLASRDFDLS 91
           +  +  + IF+V+ A  +   D F +  N+L +   + S  G+++  M+F + +R  DLS
Sbjct: 23  VQRFGTLAIFLVLVAVATWWSDSFLTRGNLLNVLRQVASTAGIMAVGMLFVILTRGIDLS 82

Query: 92  VGSTVAFAGVL----CAMVLNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTL 147
           VGS +A   VL    CAM+   TG T   ++     G   G V G  IAYLR+ + + +L
Sbjct: 83  VGSVMALGSVLTGYFCAMLGYGTGATIFLVLLC---GAACGLVTGGFIAYLRLPSFVMSL 139

Query: 148 ATMEIVRGLGFIVSHGQAVGVSSD--TFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQT 205
           A M + RGL  I+S G+ + +S     F + G     G+  P+ +    +I  GV+LN T
Sbjct: 140 AMMAVARGLSLIISEGRPIPLSDAGAAFSSFGSGFVLGIPQPVILMFAIYIAGGVVLNFT 199

Query: 206 VYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGF 265
            +GR   AIG N EA RL+GI V R  V +++I G +  LAG+I ASR   G      G 
Sbjct: 200 RFGRVITAIGSNEEAVRLSGIAVPRYIVAVYVISGLLAGLAGIIAASRTGVGSAQVGIGA 259

Query: 266 ELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAA 325
           ELNVI+A V+GG SL+GG+  +   ++G L+MG + N+MNL  +  ++Q +  GAI++ A
Sbjct: 260 ELNVIAAVVIGGASLMGGKGGVINTLLGALVMGIITNIMNLAGVPGYHQQVYMGAIIVVA 319

Query: 326 VLL 328
           +LL
Sbjct: 320 MLL 322


Lambda     K      H
   0.326    0.139    0.396 

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: 336
Number of extensions: 27
Number of successful extensions: 6
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: 331
Length adjustment: 28
Effective length of query: 310
Effective length of database: 303
Effective search space:    93930
Effective search space used:    93930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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