GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Sinorhizobium meliloti 1021

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Smeli:SM_b20972
          Length = 391

 Score =  309 bits (791), Expect = 1e-88
 Identities = 181/384 (47%), Positives = 239/384 (62%), Gaps = 19/384 (4%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA + +D++ K +     G    +  I L+I DGEF+  +GPSGCGKST LR +AGLE +
Sbjct: 1   MATIRIDNLRKSF-----GSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENL 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
             G +RL DR +  + +  RDIAMVFQ+YALYPH +VR N+SFGL  + G+  +EI +RV
Sbjct: 56  DGGSIRLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALN-GMKRNEIDRRV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
               ++L I++LLDRKP QLSGGQ+QRVA+GRAIVR+P++FL+DEPLSNLDA LR  MR 
Sbjct: 115 NNAAEILRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRV 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           EL  L   LGVT +YVTHDQ EAMT+ DRV VLD G + Q GTPL+ ++RP NLFVAGFI
Sbjct: 175 ELAALHERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFI 234

Query: 241 GEPSMNLFDGSLSGD-----TFRGDGFDYPLSGATR--DQLGGASGLTLGIRPEDVTVGE 293
           G P MN     ++       T  G G   P++  TR  + L     +TLGIRP+ + +  
Sbjct: 235 GSPRMNFLPAGVAEQAATRVTLAGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLELTS 294

Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353
                      V +VE  G E+ VH+R V+G  G   TA   G   V + D+  +  P +
Sbjct: 295 PEEAH--LAGTVRLVERLGTESHVHIR-VEG--GGDLTAVVRGTHPVASRDQVHLRLPPE 349

Query: 354 AIHLFDGETGDALKNRELPSNRAI 377
             HLFD E G A+  R  P  +A+
Sbjct: 350 HCHLFDAE-GTAIARRLDPETKAL 372


Lambda     K      H
   0.316    0.136    0.384 

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: 472
Number of extensions: 27
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: 383
Length of database: 391
Length adjustment: 30
Effective length of query: 353
Effective length of database: 361
Effective search space:   127433
Effective search space used:   127433
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: 42 (22.0 bits)
S2: 50 (23.9 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