GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Pedobacter sp. GW460-11-11-14-LB5

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__Pedo557:CA265_RS16020
          Length = 250

 Score =  110 bits (275), Expect = 3e-29
 Identities = 74/234 (31%), Positives = 122/234 (52%), Gaps = 17/234 (7%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           +++I+D+ K F G   L G+    E G    +IG +G+GKTT    + GL+QPD+G+   
Sbjct: 1   MIEIKDIYKSFSGNDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPDSGSVLY 60

Query: 65  DGKPYSPSAPHE--VAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122
           DG+ ++P    +    +  I   FQ   LF  MTV EN+M   ++ T Q           
Sbjct: 61  DGRDFTPMTYEQRIEVRKEIGMLFQGSALFDSMTVEENIMFPLNMFTDQ----------- 109

Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182
           +R+E+    E+    L+ V +    K     LS G ++R+ IARA++ +P+ L  DEP +
Sbjct: 110 SRKEKL---ERVDFCLERVNLAGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNS 166

Query: 183 GMNATEKLGLRELLVKIQAEGK-TILLIEHDVKLMMGLCNRITVLDYGKPIAEG 235
           G++    + + EL+ +I  E K T +++ HD+  +MG+ + I  L  GK   EG
Sbjct: 167 GLDPKTSIVIDELIQEITEEYKTTTIVVTHDMNSVMGIGDYILFLHEGKKFWEG 220


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: 142
Number of extensions: 9
Number of successful extensions: 4
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: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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: 46 (22.3 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