GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Aa in Sinorhizobium meliloti 1021

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SMc01979 SMc01979 sugar transport system permease ABC transporter protein

Query= uniprot:C8WUQ9
         (301 letters)



>FitnessBrowser__Smeli:SMc01979
          Length = 277

 Score =  149 bits (376), Expect = 7e-41
 Identities = 87/270 (32%), Positives = 156/270 (57%), Gaps = 12/270 (4%)

Query: 39  RIVIWCVIVMVLLPMWFVVIASFNPSNSYIS--FSLFPSNASLANYKALFQGGQFWTWVR 96
           R+ +   I   L P+++++  +  P++   S    L+PS ASL ++  + +   F  + R
Sbjct: 13  RLAVLAYIAFALFPLFWLLKVAVTPNDLLYSEGIRLWPSRASLEHFDFVLRHSAFPVFFR 72

Query: 97  NSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTLLLL-QMFPNILAIAAFYTALA 155
           NSL+V    A+  + + ++S +A S+ RF G KY L+TL+LL QMFP ++ +A  +  L+
Sbjct: 73  NSLIVSGSTAVIVTILASLSGYALSRFRFRG-KYWLVTLMLLTQMFPLVMLVAPIFKILS 131

Query: 156 KLNMIDMLGSYILVMLGTSAFNI----WLLKGYMDSVPKELDEAAVIDGATTWQRFIHVT 211
            L + + L   ++V    +AFN+    +L++ + D +PK+L+EAA+IDGAT +  F  + 
Sbjct: 132 PLGLTNSLTGLVVVY---TAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQFVAFRQII 188

Query: 212 LPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYNLISGQFAKNWGEFAAA 271
           LPL+ P +           +SE +F+  ++      T  VG+ + +S +F+ ++G+  AA
Sbjct: 189 LPLTLPGIAATLGFVFTAAWSELLFSLMLISGNAQATFPVGLLSFVS-KFSVDFGQMMAA 247

Query: 272 ALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301
            +L+ +P  + F + QRYL +GL AG+VKG
Sbjct: 248 GVLALIPACLFFLLIQRYLVQGLTAGAVKG 277


Lambda     K      H
   0.328    0.136    0.417 

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: 209
Number of extensions: 9
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: 301
Length of database: 277
Length adjustment: 26
Effective length of query: 275
Effective length of database: 251
Effective search space:    69025
Effective search space used:    69025
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 (21.8 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