GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Pseudomonas fluorescens GW456-L13

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PfGW456L13_122 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_122
          Length = 427

 Score =  249 bits (637), Expect = 7e-71
 Identities = 155/353 (43%), Positives = 212/353 (60%), Gaps = 48/353 (13%)

Query: 4   TKTNWIIGAVALLVLPLILQSFGNAWVR-IADLALLYVLLALGLNIVVGYAGLLDLGYVA 62
           ++  WII    ++V+ ++   F N+++  +  L L+YVLL LGLNIVVG AGLLDLGYVA
Sbjct: 95  SRLRWIIPL--MIVIAVVFPFFSNSYLLGVVILGLIYVLLGLGLNIVVGLAGLLDLGYVA 152

Query: 63  FYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLK 122
           FYA+GAY  AL    +L   F               W V+P+AA+ A   G +LG P L+
Sbjct: 153 FYAIGAYGLAL-GYQYLGLGF---------------WTVLPLAAITAGLAGCILGFPVLR 196

Query: 123 LRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL------ 176
           L GDYLAIVTLGFGEIIR+ LNN    + LT GP G+        FG++ GKR       
Sbjct: 197 LHGDYLAIVTLGFGEIIRLILNNW---LTLTGGPNGMAA-PLPTFFGIEFGKRAKEGGVP 252

Query: 177 --EVFGFDINSVTLYYYLFLVL--VVVSVI-ICYRLQDSRIGRAWMAIREDEIAAKAMGI 231
             E FG   N    YY+++ VL  VV++V+ I +RL    +GRAW A+REDEIA ++MG+
Sbjct: 253 FHEFFGIAYNPDVKYYFIYAVLFLVVLAVLHIKHRLTRMPVGRAWEALREDEIACRSMGL 312

Query: 232 NTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVI 291
           N   +KL AF +GAS  G++G  F  +QGFV+P SF+  ES +I+A+VVLGG+G   GV+
Sbjct: 313 NHVLVKLSAFTIGASTAGLAGVFFATYQGFVNPTSFTFFESALILAIVVLGGMGSTIGVV 372

Query: 292 LGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
           + A +L+  PE+LR                A  R LL  + M+++M+ RPRGL
Sbjct: 373 IAAFVLTVAPELLR--------------GFAEYRVLLFGILMVLMMIWRPRGL 411


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: 431
Number of extensions: 20
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: 427
Length adjustment: 31
Effective length of query: 327
Effective length of database: 396
Effective search space:   129492
Effective search space used:   129492
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 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