GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Echinicola vietnamensis KMM 6221, DSM 17526

Align NatA, 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 Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Cola:Echvi_3653
          Length = 290

 Score = 92.8 bits (229), Expect = 7e-24
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 31/225 (13%)

Query: 29  EARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQPHQIAQQGM 88
           + ++ ++QG    L GP+G+GKT+   ++S  + PDKG +  +GE            Q  
Sbjct: 20  DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGE------------QWF 67

Query: 89  VRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEE-----KQLQEQA--M 141
             +F   + +S            +++ G  F    L P + VKE      K  +++A  M
Sbjct: 68  DASF--GKNVS----------PGRRKLGYLFQDYSLFPNMTVKENIAFALKNAKDKAYLM 115

Query: 142 FLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICDR 201
            LLES+GL          LSGGQ++ + + RAL   P ++LLDEP + ++P + + + + 
Sbjct: 116 ELLESMGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEY 175

Query: 202 ILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAE 246
           IL  +R+  +T +++ H+   I+ L DR+  L  G+ L   TP E
Sbjct: 176 ILAIHRKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKE 220


Lambda     K      H
   0.319    0.136    0.391 

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: 159
Number of extensions: 4
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 290
Length adjustment: 25
Effective length of query: 235
Effective length of database: 265
Effective search space:    62275
Effective search space used:    62275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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