GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Sinorhizobium meliloti 1021

Align ABC transporter permease (characterized, see rationale)
to candidate SMc02359 SMc02359 high-affinity branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Smeli:SMc02359
          Length = 296

 Score =  172 bits (436), Expect = 9e-48
 Identities = 115/305 (37%), Positives = 172/305 (56%), Gaps = 22/305 (7%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           M   +Q +I+ L LG  YAL+ALG  ++YGI++L+NFA+GE++M+   T +   G     
Sbjct: 1   MAFAIQFVIDVLSLGGAYALMALGLVIIYGILRLVNFAYGELIMVAGYTMFLASGS---- 56

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
             G P W+++    ++A  +A     + +  A+RP+R+    A LIT+   S LLQ  A+
Sbjct: 57  --GLP-WIVM---AVLAVGMAILFGIITDYAAFRPVRAKSVTAVLITSFAFSNLLQNAAL 110

Query: 121 IIWKPNYKPYPTMLP---SSPFEIGGAFITPTQILILGVTAVAL-ASLVYLVNHTNLGRA 176
           +   P  +  P  LP   S    IGGA ITP + LI    ++AL A + +L+  T LG A
Sbjct: 111 LFISPRPRNVP--LPDIFSQTVSIGGA-ITPVRNLITIAASIALLAGVAFLMRRTTLGIA 167

Query: 177 MRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAF 236
           MRA A N  +A ++GV  +++IS+ F +   LA + GI++    GT    +G  P L AF
Sbjct: 168 MRAAATNFTMARMLGVPANLIISSAFALSGFLAGVVGILWIGRIGTVVPGIGLEPLLVAF 227

Query: 237 TAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLR 296
            A V GG+ +L GAVVGG LL LI+   +    TL+  LL   + D F F ++I+IL  R
Sbjct: 228 IATVIGGMRSLPGAVVGGFLLALIDTTLN---YTLSQDLL--KFRDAFTFSLVILILLWR 282

Query: 297 PSGLL 301
           P GL+
Sbjct: 283 PDGLI 287


Lambda     K      H
   0.327    0.142    0.419 

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: 219
Number of extensions: 11
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: 309
Length of database: 296
Length adjustment: 27
Effective length of query: 282
Effective length of database: 269
Effective search space:    75858
Effective search space used:    75858
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