GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Desulfovibrio vulgaris Miyazaki F

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 8502038 DvMF_2751 inner-membrane translocator (RefSeq)

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__Miya:8502038
          Length = 301

 Score =  184 bits (468), Expect = 2e-51
 Identities = 107/289 (37%), Positives = 178/289 (61%), Gaps = 14/289 (4%)

Query: 7   QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT-FGVNIWLS- 64
           Q + NG+AVG I AL A+G T+ YG+L+L NFAHGD  T+GAYL F + T FG++ ++S 
Sbjct: 6   QQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTLFTAFGLSGFVSG 65

Query: 65  ------MIVAVVGTVGVM-LLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWG 117
                 ++V V+G V ++  L E++ +  +RS  ++  + ++ ++G ++F +N ++LI+G
Sbjct: 66  PGGVLLVLVMVMGLVALIGFLLERVAYRPLRS--SSRLSAVVSALGASIFFQNAVMLIYG 123

Query: 118 GRNQNYNLPITPA--LDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADD 175
            + Q Y   I P+  L I G+ VP  +++++A ++  + AL++  Q T+IG A+RA A D
Sbjct: 124 AKFQVYPNDIRPSYVLSIMGIDVPLVRIMMIAASLGLMLALYWFTQRTRIGAAIRATAID 183

Query: 176 LDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITA-VRPNMGWFLILPLFASVILGG 234
              AK+ GIDV +VI   ++I   +  + G M GL    V   MGW   L  F + ILGG
Sbjct: 184 QGAAKLMGIDVNRVISLVFMIGPALGGVAGVMVGLYYGQVDFTMGWVYGLKAFTAAILGG 243

Query: 235 IGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
           IGN  GA+    ++G+++ +   ++   +K  +A L++IL+L+IRP GL
Sbjct: 244 IGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGL 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: 250
Number of extensions: 19
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: 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