GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Acidovorax sp. GW101-3H11

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_1937 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1937
          Length = 279

 Score =  210 bits (535), Expect = 2e-59
 Identities = 106/257 (41%), Positives = 165/257 (64%), Gaps = 6/257 (2%)

Query: 2   SQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGT 61
           + TLL  +++S RFGG+ A+N V   + RG+++ LIGPNGAGKTT FN+I+ +Y P TGT
Sbjct: 3   NDTLLSAQNLSVRFGGVLAVNNVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYTPTTGT 62

Query: 62  FELDGK-----PYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGA 116
               G      P +   PH+VA  GIARTFQNI LF   +VL N+++G H +   +++  
Sbjct: 63  IAYAGPGGAMLPLTDQPPHKVASLGIARTFQNIELFEHASVLHNLLIGRHTQQHSSLWAE 122

Query: 117 VFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLA 176
           +F  +  RE E   REK+++++DF+ +  +       L YG ++ +E+ARAL T+P+LL 
Sbjct: 123 MFFTRKVREGEIQAREKAEQIIDFLDLQHYRDTMVAGLPYGVRKVVELARALCTEPKLLL 182

Query: 177 LDEPAAGMNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEG 235
           LDEP++G+N  E   +   +  IQ E G T+L++EHD+ L+  + +R+  ++ G+ +A G
Sbjct: 183 LDEPSSGLNVEETDDMAFWIQDIQHELGITVLMVEHDMSLVSKVSDRVLAMNQGEVVAMG 242

Query: 236 VPADVQKNPAVIEAYLG 252
            P +VQ +P V+EAYLG
Sbjct: 243 TPREVQTHPGVVEAYLG 259


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: 194
Number of extensions: 9
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: 279
Length adjustment: 25
Effective length of query: 230
Effective length of database: 254
Effective search space:    58420
Effective search space used:    58420
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.

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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