GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Sinorhizobium meliloti 1021

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate SMc02257 SMc02257 ABC transporter permease

Query= uniprot:B2TBJ8
         (250 letters)



>FitnessBrowser__Smeli:SMc02257
          Length = 274

 Score =  144 bits (364), Expect = 1e-39
 Identities = 80/223 (35%), Positives = 129/223 (57%), Gaps = 4/223 (1%)

Query: 5   FDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRG 64
           +D+L   + +L + +  +L + F + ILG LL++ +   +V+  W     AR +  V RG
Sbjct: 47  WDWLPRYLPRLGSGILVSLAMLFSTAILGFLLAVPLGLAQVTGPWFFKAPARIFCTVIRG 106

Query: 65  SPLLIQMFLVYYGMG----QFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGL 120
           +PLL+Q++L+YYG+G    QF  IR+SFLWP LRE +   V +L +  A Y  E++RG  
Sbjct: 107 TPLLLQLWLLYYGLGSLFPQFPAIRQSFLWPYLREAWPYGVAALTVSFAAYEGEVMRGAF 166

Query: 121 MAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEV 180
             VP G++EA  + G+  + + RR+  P A+ + LP  + E VL +KST L + +TV +V
Sbjct: 167 AGVPSGELEAARAYGMGRWTMFRRIWLPRAIHRALPTLNGETVLQLKSTPLVATITVVDV 226

Query: 181 TGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRL 223
             V  ++ Q+TY T E  +  A IY+ L  ++V      E R+
Sbjct: 227 YAVISKVRQETYLTYEPLLLLAAIYMCLTAILVVAFRYFENRI 269


Lambda     K      H
   0.331    0.143    0.431 

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: 187
Number of extensions: 8
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: 250
Length of database: 274
Length adjustment: 25
Effective length of query: 225
Effective length of database: 249
Effective search space:    56025
Effective search space used:    56025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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