GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Azospirillum thiophilum BV-S

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_045585060.1 AL072_RS29555 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:A0A165KER0
         (358 letters)



>NCBI__GCF_001305595.1:WP_045585060.1
          Length = 497

 Score =  247 bits (631), Expect = 4e-70
 Identities = 149/345 (43%), Positives = 197/345 (57%), Gaps = 45/345 (13%)

Query: 12  AVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           AVA+ V+  +        + I  L L Y++L  GLNIVVG AGLLDLGYVAFYAVGAY +
Sbjct: 163 AVAIAVVLPMTPLADRMLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSY 222

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           AL+A                +    S W+ +P+A +LAAF G +LG P L+LRGDY AIV
Sbjct: 223 ALLA----------------HYFGLSFWLCLPLAGVLAAFSGVLLGFPVLRLRGDYFAIV 266

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL---------EVFGFD 182
           TLGFGEIIRI L N       T GP G+  I     FG+    R          E+FG +
Sbjct: 267 TLGFGEIIRIILVNW---YQFTGGPNGISGIPRPSFFGIAEFSRTPADGMAAFHEMFGLE 323

Query: 183 ---INSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239
              ++ +   YYL L L +V  +   R++   +GRAW A+RED+IA  ++GIN  NMKL 
Sbjct: 324 FSPLHRIVFLYYLILALALVVNVFTLRVRKLPLGRAWEALREDDIACASLGINRTNMKLA 383

Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299
           AF + A FGG +G+ F   QGF+SPESF+ +ES +I+A+VVLGG+G   GV++  +L+  
Sbjct: 384 AFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVATLLVIG 443

Query: 300 LPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
           LPE  R +A                R L     M++IML RPRGL
Sbjct: 444 LPEAFRELAD--------------YRMLAFGAGMVVIMLWRPRGL 474


Lambda     K      H
   0.328    0.144    0.430 

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: 473
Number of extensions: 23
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: 358
Length of database: 497
Length adjustment: 32
Effective length of query: 326
Effective length of database: 465
Effective search space:   151590
Effective search space used:   151590
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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