GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Cupriavidus basilensis 4G11

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 RR42_RS34785 RR42_RS34785 ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__Cup4G11:RR42_RS34785
          Length = 287

 Score =  178 bits (452), Expect = 1e-49
 Identities = 95/282 (33%), Positives = 162/282 (57%), Gaps = 3/282 (1%)

Query: 6   IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNT-FGVNIWLS 64
           +Q ++NG+ +G + +L A+GLTL YGIL + NFAHG F   GAY+++++ T  G+N WL+
Sbjct: 5   LQQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVSYYLMTSLGMNYWLA 64

Query: 65  MIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYN 124
           M  A +    + +L+++L++  +R+  A     +I +IG+ LFL  G   +WG       
Sbjct: 65  MGAAAIAVAVLSMLADRLVFHPLRN--APELHDMIAAIGIMLFLEAGAQAMWGADFHRMP 122

Query: 125 LPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSGI 184
            P    +++ G+  P  +LL++A A   +  LH  L  T  G  + A+A + + A + GI
Sbjct: 123 TPYGQMVEVMGLSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVAMAQNREGAALVGI 182

Query: 185 DVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIAA 244
           D  +V    + I+G + ++  ++Y  I  V P+MG  +I   F  +ILGG+G+  GAI  
Sbjct: 183 DATRVTLLVFAISGALAAIAATLYAPINLVYPSMGNLVITKAFVIIILGGMGSIPGAIVG 242

Query: 245 AFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLFKG 286
             IIG+ +     ++ + YK  +A  +++L+L IRP+GLF G
Sbjct: 243 GLIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGLFAG 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: 250
Number of extensions: 17
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: 287
Length adjustment: 26
Effective length of query: 262
Effective length of database: 261
Effective search space:    68382
Effective search space used:    68382
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: 47 (22.7 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