GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Sinorhizobium meliloti 1021

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SM_b20232 SM_b20232 sugar ABC transporter permease

Query= uniprot:A8LLL5
         (334 letters)



>FitnessBrowser__Smeli:SM_b20232
          Length = 314

 Score =  122 bits (307), Expect = 9e-33
 Identities = 81/280 (28%), Positives = 144/280 (51%), Gaps = 15/280 (5%)

Query: 51  IRPWIFLFPALFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAM 110
           I  ++F+ P    L ++LG P+  +L LS+ E    GGY +VG  NY +M ++P FW+  
Sbjct: 27  IAGYLFVLPDALGLFIFLGVPMALSLVLSVFEVNGFGGYSFVGARNYLRMWNDPLFWKGA 86

Query: 111 RNNMFWLIVVPALSTAFGLLAAQLTDRI-KWGNVAKSIIFMPMAISFVGASVIWKLVYDG 169
           R    +  ++  L    GL  A L  R  ++  + +S+ F P  +S V  +++W+ +   
Sbjct: 87  RVTALYAAMLVPLLYVCGLGLALLVQRTDRFNAIMRSMFFAPHMVSLVVVALVWQFMV-- 144

Query: 170 RPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIP 229
                ++IG+++ +   L    ++ L  P +    +++V VW   GF M+I    L+ IP
Sbjct: 145 ----VDKIGVVSRLTAALDIGGISLLGDPNFALITIVLVSVWFLMGFYMLIFLGGLQDIP 200

Query: 230 EETIEAAIIDGASPLQIFFKIKVPQIMPT---VVVVWTTITLVVLKVFDIVFAMTNG--Q 284
            +  EAA+IDGA  +  F+ I +P + PT   V++V     +   + FDI++ MT G   
Sbjct: 201 RQYYEAAMIDGAGAIARFWFITLPLLKPTSFFVIMVSMVAAVAGAQAFDIIYVMTKGGPA 260

Query: 285 WETQVLANYMFDKLFRANDWGVGSASA---MVIMLLVTPI 321
             T VL  Y++ + F    +G  +A A   +V +++VT +
Sbjct: 261 NATSVLIVYIYQQAFGFGAFGYAAAMASILVVALMIVTAV 300


Lambda     K      H
   0.329    0.143    0.455 

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: 270
Number of extensions: 21
Number of successful extensions: 4
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: 334
Length of database: 314
Length adjustment: 28
Effective length of query: 306
Effective length of database: 286
Effective search space:    87516
Effective search space used:    87516
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