GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__Cola:Echvi_3653
          Length = 290

 Score =  157 bits (398), Expect = 3e-43
 Identities = 91/228 (39%), Positives = 136/228 (59%), Gaps = 12/228 (5%)

Query: 1   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60
           M ++ LQ   KA G  +   DI L I +GEF+   GPSG GK++ LRMI+GL T   G L
Sbjct: 1   MINIDLQKSLKANGPAM-DLDIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHL 59

Query: 61  FIGEKRMNDTP------PAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRV 114
            +  ++  D        P  R +G +FQ Y+L+P+++V EN++F LK A  K  ++    
Sbjct: 60  SVNGEQWFDASFGKNVSPGRRKLGYLFQDYSLFPNMTVKENIAFALKNAKDKAYLM---- 115

Query: 115 NQVAEVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRI 174
            ++ E + L HL D  PK LSGGQ+QRVA+ R L  +P + LLDEPLS LD ++R +++ 
Sbjct: 116 -ELLESMGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQE 174

Query: 175 EISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELY 222
            I  +H++   T I V+HD  E + L+D+I+ LD G+V +   P E +
Sbjct: 175 YILAIHRKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKEFF 222


Lambda     K      H
   0.320    0.137    0.393 

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: 236
Number of extensions: 10
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: 371
Length of database: 290
Length adjustment: 28
Effective length of query: 343
Effective length of database: 262
Effective search space:    89866
Effective search space used:    89866
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 (21.8 bits)
S2: 49 (23.5 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