GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Sinorhizobium meliloti 1021

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate SM_b21605 SM_b21605 sugar uptake ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Smeli:SM_b21605
          Length = 362

 Score =  330 bits (845), Expect = 5e-95
 Identities = 174/362 (48%), Positives = 238/362 (65%), Gaps = 7/362 (1%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M+ + +  +S +FGAV V+  ++++I  GEF V +G SGCGKSTLL  IAGL + + G+I
Sbjct: 1   MSGIKLTGVSKSFGAVKVIHGVDIEIGQGEFAVFVGPSGCGKSTLLRMIAGLEETTGGEI 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I   +VT +EP  RG+ MVFQSYALYP ++V  N++F L +A+ P AEIE++VK A+EI
Sbjct: 61  RIDAEDVTHKEPSKRGVAMVFQSYALYPHLSVFDNMAFSLSIARRPKAEIEQKVKAAAEI 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           L++   L  KPS+LSGGQRQRVAIGRA+VR+  VFLFDEPLSNLDA+LR ++R+EI RLH
Sbjct: 121 LRLSDYLDSKPSQLSGGQRQRVAIGRAIVREPRVFLFDEPLSNLDAELRVKMRMEIARLH 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           + +  TM+YVTHDQ+EA+TLADRI V+K+GV+QQ   P+ +Y  P+N+FVAGFIGSP MN
Sbjct: 181 RQIGATMVYVTHDQVEAMTLADRIVVLKAGVVQQTGAPLELYRNPDNMFVAGFIGSPGMN 240

Query: 241 FFRGEVEPKDGRSFV----RAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296
           F +  V P  G         A G+ F++   PA T    G+++ +G+RPEH+ + E   G
Sbjct: 241 FLKARVVPGSGDRLTIELHDAPGVPFEI---PARTGPAVGEEIFVGVRPEHITLGEREGG 297

Query: 297 EPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAE 356
                    IEE  G   L  LT  G+ M++   G+ R  P   VRL+        F+  
Sbjct: 298 VGLDVTAEFIEELGGTGYLHALTVTGEEMTIECRGEERPQPKQAVRLTLAPEEMFAFEGS 357

Query: 357 SE 358
            E
Sbjct: 358 GE 359


Lambda     K      H
   0.320    0.137    0.392 

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: 404
Number of extensions: 19
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: 361
Length of database: 362
Length adjustment: 29
Effective length of query: 332
Effective length of database: 333
Effective search space:   110556
Effective search space used:   110556
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