GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pseudomonas putida KT2440

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_2748 PP_2748 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Putida:PP_2748
          Length = 266

 Score =  187 bits (474), Expect = 3e-52
 Identities = 107/271 (39%), Positives = 157/271 (57%), Gaps = 9/271 (3%)

Query: 1   MMSPVTNTMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCI 60
           M + ++       LL+V ++S+ F G+ AI+D SF  +RG+I ALIGPNGAGK+++ N +
Sbjct: 1   MAARISGARGMSALLEVRNVSLSFKGVKAISDLSFSVRRGEICALIGPNGAGKSSLLNIL 60

Query: 61  TGFYKPTMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQ 120
            G Y+   G + F  +        R P         + RTFQN  LF  ++VL+NLL   
Sbjct: 61  NGVYRADAGQLFFATEP------LRRPHPLQAARLGIGRTFQNNALFKKMSVLDNLLTGL 114

Query: 121 HNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRL 180
            ++  ++  Y +   +G+   +REA    E A   L   +L    D   G L YG Q+R+
Sbjct: 115 -SRFQRS--YFLEQALGLPRARREARAFAERAEQVLAFLELQPWRDVAVGSLAYGLQKRV 171

Query: 181 EIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISD 240
           E+ RA+   P LL LDEP AG+N  E   ++  +  I  + GT+++LIEHD+ VVM +S 
Sbjct: 172 ELGRALIAQPTLLLLDEPMAGMNAEEKQDMSRFIADINRDLGTTVILIEHDIQVVMGLSS 231

Query: 241 HVVVLEYGQKISDGTPDHVKNDPRVIAAYLG 271
           HVVVL+YG+K+ DGTP  V+ +P VIAAYLG
Sbjct: 232 HVVVLDYGRKVGDGTPAEVQANPDVIAAYLG 262


Lambda     K      H
   0.318    0.136    0.386 

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: 185
Number of extensions: 5
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: 292
Length of database: 266
Length adjustment: 26
Effective length of query: 266
Effective length of database: 240
Effective search space:    63840
Effective search space used:    63840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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