GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Desulfovibrio vulgaris Hildenborough

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 206140 DVU0715 branched-chain amino acid ABC transporter, ATP binding protein

Query= uniprot:D8IUY7
         (241 letters)



>MicrobesOnline__882:206140
          Length = 255

 Score =  124 bits (312), Expect = 1e-33
 Identities = 78/251 (31%), Positives = 133/251 (52%), Gaps = 17/251 (6%)

Query: 4   NILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGH 63
           ++L ++ L+  +GG+ AV  +  +V+EG +V LIG NGAGKTT    ITG        G 
Sbjct: 2   SLLSLRNLTKTFGGLVAVNSVSFDVDEGSIVGLIGPNGAGKTTVFNLITGNYKPD--SGD 59

Query: 64  IEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADI--- 120
           I + G+ +KG  +  +V+  +A   +   +F  MS+ EN+L G +     G  +A +   
Sbjct: 60  IFFDGRAIKGLLTHRIVQMGIARTFQTIRLFQNMSVMENVLAGCHCRMTAGVFSAMLGTA 119

Query: 121 ----DKWFAV--------FPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPS 168
               ++  A+        F  L ++   +A  LS G Q++L +ARAL + P+ ++LDEP+
Sbjct: 120 GHRREEKRAIERAVRELEFVGLADQHDNLAKNLSYGNQRLLEIARALATDPRFIILDEPA 179

Query: 169 MGLSPIMVEKIFEVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQML 228
            G++      +   IR +  +GI++LL+E +  L ++   +  V+E G +  +G    + 
Sbjct: 180 GGMNDQETAALIGTIRAIRDRGISVLLIEHDMSLVMKVCEKLVVLEYGALIAEGTPSVIK 239

Query: 229 DDPRVKAAYLG 239
            DPRV  AYLG
Sbjct: 240 RDPRVIEAYLG 250


Lambda     K      H
   0.317    0.134    0.365 

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: 143
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: 241
Length of database: 255
Length adjustment: 24
Effective length of query: 217
Effective length of database: 231
Effective search space:    50127
Effective search space used:    50127
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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