GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Azospirillum brasilense Sp245

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS08240 AZOBR_RS08240 ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__azobra:AZOBR_RS08240
          Length = 505

 Score =  246 bits (629), Expect = 7e-70
 Identities = 147/325 (45%), Positives = 191/325 (58%), Gaps = 45/325 (13%)

Query: 32  IADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFP 91
           I  L L Y++L  GLNIVVG AGLLDLGYVAFYAVGAY +AL+A      ++  F     
Sbjct: 175 IGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLA------HYFGF----- 223

Query: 92  NGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVN 151
                S W+ +P+A  LAA  G +LG P L+LRGDY AIVTLGFGEIIRI L N      
Sbjct: 224 -----SFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINW---YQ 275

Query: 152 LTNGPKGLGQIDSVKVFGLDLGKRL---------EVFGFD---INSVTLYYYLFLVLVVV 199
            T GP G+  I     FG+    R          E+FG +   ++ +   YYL LVL +V
Sbjct: 276 FTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALV 335

Query: 200 SVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQ 259
             +   R++   +GRAW A+RED+IA  ++GIN  NMKL AF + A FGG +G+ F   Q
Sbjct: 336 VNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQ 395

Query: 260 GFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRL 319
           GF+SPESF+ +ES +I+A+VVLGG+G   GV++ A L+  LPE  R +A           
Sbjct: 396 GFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELAD---------- 445

Query: 320 DSAILRQLLIALAMIIIMLLRPRGL 344
                R L   + M++IML RPRGL
Sbjct: 446 ----YRMLAFGMGMVLIMLWRPRGL 466


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: 469
Number of extensions: 25
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: 358
Length of database: 505
Length adjustment: 32
Effective length of query: 326
Effective length of database: 473
Effective search space:   154198
Effective search space used:   154198
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: 51 (24.3 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