GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Azospirillum brasilense Sp245

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 AZOBR_RS21005 AZOBR_RS21005 branched-chain amino acid ABC transporter

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__azobra:AZOBR_RS21005
          Length = 294

 Score =  164 bits (414), Expect = 3e-45
 Identities = 96/282 (34%), Positives = 165/282 (58%), Gaps = 6/282 (2%)

Query: 6   IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTF-GVNIWLS 64
           +QL+V+G+ +G I AL ++GLTL +G+ R+ NFAHGDF+ +G YLT+ +N++ G++ +L 
Sbjct: 6   VQLVVSGLLLGGIYALISIGLTLIFGVSRIKNFAHGDFVMVGMYLTYVLNSWSGLDSYLV 65

Query: 65  MIVAVVGTVGVMLLSEKLLWSRMRSIR-ANSTTLIIISIGLALFLRNGIILIWGGR-NQN 122
           +++    T  + L    L W+ +R I+ A     I  ++GL L L+N  ++I+GG     
Sbjct: 66  LLIV---TPLMFLFGLFLSWAIIRPIQGAPQVAQIFATVGLGLVLQNVTLMIFGGDFRTT 122

Query: 123 YNLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVS 182
            ++     L I  + +P   L+  A+A+  +  ++  L+ +  GKAMRAVA D   A + 
Sbjct: 123 ASVFAGKVLRIGDIALPAPLLIAFAVAMAVVAVIYLFLKTSYTGKAMRAVAQDRRSASLM 182

Query: 183 GIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAI 242
            IDV+ +  +T+ +      L G++   +  V P +G  L+L  F  V+LGG+G+  GA+
Sbjct: 183 SIDVKGIDLFTFGLGTACAGLTGALLAPMFPVYPTVGINLVLIAFVVVVLGGLGSIAGAL 242

Query: 243 AAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284
                IG+++ +S  F+GS+ +Q    L+ + VLL+RP GLF
Sbjct: 243 IGGLAIGLIETLSGFFIGSEMRQMAYFLVFLAVLLLRPAGLF 284


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: 246
Number of extensions: 15
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: 294
Length adjustment: 26
Effective length of query: 262
Effective length of database: 268
Effective search space:    70216
Effective search space used:    70216
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 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