GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Azospirillum thiophilum BV-S

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_045585626.1 AL072_RS27695 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>NCBI__GCF_001305595.1:WP_045585626.1
          Length = 292

 Score =  169 bits (427), Expect = 9e-47
 Identities = 94/280 (33%), Positives = 168/280 (60%), Gaps = 4/280 (1%)

Query: 7   QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT-FGVNIWLSM 65
           Q I NG+  G    L A GLTL +G+LR+ NFAHG+F  LGAY+T+F+ T FG++   + 
Sbjct: 8   QQIANGLVNGMAYVLIATGLTLVFGVLRIVNFAHGEFYMLGAYITYFIGTLFGLDYLAAA 67

Query: 66  IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYNL 125
            ++ V   G+ + + KL++  +R  R +  T+++ S+GLAL + NG  L++G   +    
Sbjct: 68  AISAVVVAGLGIAANKLIFWPLR--RDHEFTILLSSLGLALLIANGGELLFGADPKYVES 125

Query: 126 PITP-ALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSGI 184
           P     L+I  V + Q ++LV A AV+++ A++  ++ ++ GK MRA A + D A ++GI
Sbjct: 126 PFADEVLEIGTVTLTQQRVLVFAAAVVALVAVYLFIRYSRFGKMMRATAQNPDGAALTGI 185

Query: 185 DVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIAA 244
           ++  V  +T+ +A  + +L G++ G    + P +G + +L  F  VI+GG+G+  GA+ A
Sbjct: 186 NIGLVHTYTFALACGLAALSGALVGPTVMIFPTIGNWAVLKGFIVVIMGGLGSVTGALFA 245

Query: 245 AFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284
             ++G+++ +   ++   + + +   ++I VLL RP GLF
Sbjct: 246 GLLLGVIESLGGGYISLGFMEAIGYAMIIAVLLWRPNGLF 285


Lambda     K      H
   0.328    0.144    0.426 

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: 240
Number of extensions: 14
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: 288
Length of database: 292
Length adjustment: 26
Effective length of query: 262
Effective length of database: 266
Effective search space:    69692
Effective search space used:    69692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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