GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Azospirillum brasilense Sp245

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS22350 AZOBR_RS22350 ABC transporter

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__azobra:AZOBR_RS22350
          Length = 268

 Score =  221 bits (564), Expect = 9e-63
 Identities = 115/250 (46%), Positives = 165/250 (66%), Gaps = 2/250 (0%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           + + R VS RFGG+QAL  VG +I +G+++ +IGPNGAGKT+  N I+G Y+P  G    
Sbjct: 1   IFEARGVSLRFGGVQALTDVGFSIRKGELFSIIGPNGAGKTSMVNCISGRYRPTDGKVYF 60

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVF-GAVFRHKAA 123
            G+  +   P+  A  GI RTFQN+ LFG MTVL+N+MVG H   K N F G+++    A
Sbjct: 61  KGQDITGMTPNHRASLGIGRTFQNLALFGHMTVLDNIMVGRHHLLKNNFFTGSLYWLTGA 120

Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183
           R+EE A R + ++++DF+ I    K TA  LSYG ++R+E+ARA+A  P L+ LDEP AG
Sbjct: 121 RKEELAHRREVEEIIDFLEIQHVRKATAGTLSYGLRKRVELARAIALKPDLILLDEPMAG 180

Query: 184 MNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242
           MN  EK  +   +V +  E G T+++IEHD+ ++M + +R+ VL++GK IAEG P +V  
Sbjct: 181 MNLEEKEDMARYIVDLNEEFGMTVVMIEHDMGVVMDISHRVIVLEFGKKIAEGTPEEVLA 240

Query: 243 NPAVIEAYLG 252
           +P V  AYLG
Sbjct: 241 DPRVKRAYLG 250


Lambda     K      H
   0.320    0.138    0.394 

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: 188
Number of extensions: 13
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: 255
Length of database: 268
Length adjustment: 25
Effective length of query: 230
Effective length of database: 243
Effective search space:    55890
Effective search space used:    55890
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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