GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Desulfovibrio vulgaris Hildenborough

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 206138 DVU0713 branched-chain amino acid ABC transporter, permease protein

Query= TCDB::Q8YXD0
         (288 letters)



>MicrobesOnline__882:206138
          Length = 301

 Score =  181 bits (459), Expect = 2e-50
 Identities = 101/292 (34%), Positives = 169/292 (57%), Gaps = 18/292 (6%)

Query: 6   IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFV----------- 54
           +Q + NG+AVG I AL A+G T+ YG+L+L NFAHGD  T+GAYL F V           
Sbjct: 5   LQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTVFAALGLSGHVS 64

Query: 55  NTFGVNIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIIL 114
               V +  +M++ +V  +G +L  E++ +  +RS  ++  + ++ ++G ++F +N ++L
Sbjct: 65  GAVAVLLVTTMVMGLVALIGYLL--ERVAYRPLRS--SSRLSAVVSALGASIFFQNAVML 120

Query: 115 IWGGRNQNYNLPITP--ALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAV 172
           I+G + Q Y   I P  A+  FG+ +P  ++++   +V  +  LH+ +  T+ G A+RAV
Sbjct: 121 IYGAKFQVYPNDIRPTMAVSFFGMDIPLVRIMMFGASVALMLLLHFFIHRTRTGTAIRAV 180

Query: 173 ADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITA-VRPNMGWFLILPLFASVI 231
           A D   AK+ GIDV +VI   ++I   +    G M GL    +   MGW   L  F + I
Sbjct: 181 AIDQGAAKLMGIDVNRVIALVFMIGPALGGAAGVMVGLYYGQIDFTMGWVYGLKAFTAAI 240

Query: 232 LGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
           LGGIGN  GA+    ++G+++ +   ++   +K  +A L++IL+L+IRP GL
Sbjct: 241 LGGIGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGL 292


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: 253
Number of extensions: 20
Number of successful extensions: 4
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: 301
Length adjustment: 26
Effective length of query: 262
Effective length of database: 275
Effective search space:    72050
Effective search space used:    72050
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