GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Marinobacter adhaerens HP15

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 GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__Marino:GFF3113
          Length = 307

 Score =  150 bits (380), Expect = 3e-41
 Identities = 89/292 (30%), Positives = 160/292 (54%), Gaps = 17/292 (5%)

Query: 7   QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT----FGVNIW 62
           Q ++NG+ +GS  AL A+G T+ YGI+ + NFAHG+   +GAY      T     G+  W
Sbjct: 9   QQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAALGI-AW 67

Query: 63  LSMIVAVVGTVGVMLLSEKLLWS----RMRSIRANSTTLIIIS-IGLALFLRNGIILIWG 117
           L +I+ +V  +  M++S  + W+      R +R     + +IS IG+++FL+N + L  G
Sbjct: 68  LPLIL-IVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNYVHLAQG 126

Query: 118 GRNQNYNLPITPAL-----DIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAV 172
            RN  +   I         D F + +   Q+ +    ++ + AL   +  ++ G+A RAV
Sbjct: 127 SRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTGRACRAV 186

Query: 173 ADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLIT-AVRPNMGWFLILPLFASVI 231
           + DL +A + GID  ++I  T++I   + ++ G + G+   +V P  G+   L  F + +
Sbjct: 187 SQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLKAFTAAV 246

Query: 232 LGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
           LGGIG+  GA+    I+G+ + +++ +L  +YK  ++  ++IL+LL +P GL
Sbjct: 247 LGGIGSIPGAMLGGLILGVAESMTSGYLSGEYKDVISFSLLILILLFKPTGL 298


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: 222
Number of extensions: 12
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: 307
Length adjustment: 26
Effective length of query: 262
Effective length of database: 281
Effective search space:    73622
Effective search space used:    73622
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