GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Sinorhizobium meliloti 1021

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate SMc02357 SMc02357 high-affinity branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__Smeli:SMc02357
          Length = 244

 Score =  196 bits (499), Expect = 3e-55
 Identities = 115/255 (45%), Positives = 157/255 (61%), Gaps = 16/255 (6%)

Query: 1   MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60
           MS+T L + DVS  F GL+AL+ V +++  G++ GLIGPNG+GKTT  N ITG  +  TG
Sbjct: 1   MSETRLAVNDVSVEFTGLRALDHVSLSVAAGEVVGLIGPNGSGKTTLINAITGQVKLATG 60

Query: 61  TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120
           T        S  +P E+A AG++R+FQ +R+F  MTV+ENV              A    
Sbjct: 61  TIAAGDTTLSGLSPREIALAGVSRSFQIVRIFNSMTVMENVE------------AAALAK 108

Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180
            A+R   A   E+++ LL  +G+   A      LSYGD+RR+EIARALA +P+ L LDEP
Sbjct: 109 GASRTVSA---ERAKGLLAELGLTAKADELGESLSYGDKRRVEIARALAAEPRFLLLDEP 165

Query: 181 AAGMNATEKLGLRELLVKI-QAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239
           AAGMN  E   L   L ++ +  G  +L+I+HD+ L+M LC+R+ VL  G+ IAEG  A 
Sbjct: 166 AAGMNDAETETLLHTLAELPEKRGLGLLIIDHDMGLIMRLCHRLHVLASGRTIAEGDAAH 225

Query: 240 VQKNPAVIEAYLGAG 254
           V+ +PAVIEAYLG G
Sbjct: 226 VRSHPAVIEAYLGKG 240


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: 183
Number of extensions: 7
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: 244
Length adjustment: 24
Effective length of query: 231
Effective length of database: 220
Effective search space:    50820
Effective search space used:    50820
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.

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