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_b20506 SM_b20506 L-arabinose transporter permease

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__Smeli:SM_b20506
          Length = 317

 Score =  380 bits (977), Expect = e-110
 Identities = 194/303 (64%), Positives = 236/303 (77%)

Query: 35  EYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGS 94
           E  L+VIF   F  ++LTV +F +  NMLGL  S+  IG+V+CTMMFCLASRDFDLSVGS
Sbjct: 12  EQGLLVIFAAAFVVVALTVPNFLTERNMLGLLQSVVTIGVVACTMMFCLASRDFDLSVGS 71

Query: 95  TVAFAGVLCAMVLNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEIVR 154
           TVAF+G++  M  NATG+  + ++AA+A GG++G  NG VIA  RINALITTLATM+IVR
Sbjct: 72  TVAFSGMVAVMASNATGSIVLGLLAALACGGIVGLANGIVIARFRINALITTLATMQIVR 131

Query: 155 GLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAI 214
           G   I S G+AVG++   F  L    F  V  PIWV  L FIVFG +LN+TV+G+NTLAI
Sbjct: 132 GFALIASDGRAVGINDPVFYQLSLSKFLTVPTPIWVMALFFIVFGFLLNRTVFGKNTLAI 191

Query: 215 GGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVISACV 274
           GGNPEASRLAG++V R R++IF +QG V A+AGV+LASRITSGQPNAA G EL+VISACV
Sbjct: 192 GGNPEASRLAGVDVARMRIWIFALQGLVCAVAGVLLASRITSGQPNAATGLELSVISACV 251

Query: 275 LGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKNR 334
           LGGVSL GGRAT++GVV+GVLIMG  ENVMNL+NI AFYQY+VRG ILL AVLLD +++ 
Sbjct: 252 LGGVSLAGGRATMTGVVVGVLIMGIAENVMNLLNIQAFYQYVVRGLILLIAVLLDNMRSV 311

Query: 335 GSR 337
             R
Sbjct: 312 AGR 314


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: 385
Number of extensions: 12
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: 338
Length of database: 317
Length adjustment: 28
Effective length of query: 310
Effective length of database: 289
Effective search space:    89590
Effective search space used:    89590
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: 48 (23.1 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