GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Megamonas funiformis YIT 11815

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_008537164.1 HMPREF9454_RS00035 methionine ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_000245775.1:WP_008537164.1
          Length = 353

 Score =  162 bits (409), Expect = 2e-44
 Identities = 86/231 (37%), Positives = 141/231 (61%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           I+++N+ K +      V A+ ++++ I  G  +G++G SG GK+T +R I  LE PTSG 
Sbjct: 2   IKLKNIVKTYDTPNGSVHALKDINLEIKRGEIYGIIGLSGAGKSTLVRCINMLERPTSGN 61

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           +  + + +++     +   ++ I M+FQ++ L    TV+DNIAFPLKLA   K++I+ KV
Sbjct: 62  VIVNGKDLTTMTESQLREARKDIGMIFQHFNLLSTSTVYDNIAFPLKLAGKSKEEIKAKV 121

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
           + + + +GL    ++YP +LSGGQ QR  IARAL  D KVLL DE  S LD Q  ++   
Sbjct: 122 EPLLKLVGLENKAHQYPSQLSGGQKQRVGIARALANDTKVLLCDEATSALDPQTTKAILE 181

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYP 234
           L+R I ++ +LT ++++H+   I  + +K  V+ +G  A+ GT  EI+  P
Sbjct: 182 LIRDINKKLQLTVVVITHEMQVIKDLCDKVAVLDHGVIAENGTVLEIFTNP 232


Lambda     K      H
   0.317    0.136    0.374 

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: 304
Number of extensions: 11
Number of successful extensions: 1
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: 371
Length of database: 353
Length adjustment: 29
Effective length of query: 342
Effective length of database: 324
Effective search space:   110808
Effective search space used:   110808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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