GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_3577 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3577 Branched-chain amino
           acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
          Length = 290

 Score =  220 bits (560), Expect = 3e-62
 Identities = 122/282 (43%), Positives = 167/282 (59%), Gaps = 31/282 (10%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           +EVVLKV  +  +FGG++ALSDV + +KR  ++ LIGPNGAGKTT FN +TG Y    G 
Sbjct: 2   SEVVLKVENLMMQFGGIKALSDVSLQVKRNSIFALIGPNGAGKTTVFNCLTGFYKASGGK 61

Query: 66  FEL------------AGKPYEPT------------------AVHEVAKAGIARTFQNIRL 95
            EL             G+ + PT                    H V +AG+ARTFQNIRL
Sbjct: 62  IELNVRGEQTNVIKLLGEAFRPTDFVSPKSFASRLYYKMFGGTHLVNRAGLARTFQNIRL 121

Query: 96  FAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKA 155
           F EM+ LEN++V +H+     +   +  TKG++  E+     A   L+ V +   A+  A
Sbjct: 122 FKEMSVLENLLVAQHMWVNRSMVAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANRLA 181

Query: 156 RTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQLRELIDRIRND-NRTILLIE 214
             LSYG QRRLEIARA+ T PQ+I LDEPAAG+N  E   L  +I  +R++ + T++LIE
Sbjct: 182 GELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVLIE 241

Query: 215 HDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEKVIEAYLG 256
           HD+ +VM + D + VLD+G  IAEG P  ++ + KVI AYLG
Sbjct: 242 HDMGMVMSISDHIVVLDHGNVIAEGGPEAIRNDPKVIAAYLG 283


Lambda     K      H
   0.319    0.137    0.384 

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: 216
Number of extensions: 10
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: 260
Length of database: 290
Length adjustment: 25
Effective length of query: 235
Effective length of database: 265
Effective search space:    62275
Effective search space used:    62275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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