GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Dechlorosoma suillum PS

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Dsui_3464 Dsui_3464 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__PS:Dsui_3464
          Length = 263

 Score =  167 bits (424), Expect = 2e-46
 Identities = 90/220 (40%), Positives = 135/220 (61%), Gaps = 7/220 (3%)

Query: 1   MARVLLEHIYKTY--PGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDIT 58
           M+ +L++ + K +  PG     +KD NL ++  EF   +GPSGCGK+T L  +AG +  +
Sbjct: 1   MSDILIKDVQKVFKTPGGDVTALKDINLTVKQGEFVCLLGPSGCGKSTLLNAVAGFQPPS 60

Query: 59  EGNLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQE 118
            G + I  +++    P   D  MVFQ YAL+P MTV QN+AFGL+++K  KAEID  V +
Sbjct: 61  AGEIVIEGKKILTPGP---DRGMVFQEYALFPWMTVAQNIAFGLQIQKKEKAEIDLTVNQ 117

Query: 119 AAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEI 178
              +L +    DR PK LSGG RQRVA+ R +  +  + LMDEP   LDA  R  ++ E+
Sbjct: 118 LLDLLHLKDFRDRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDEL 177

Query: 179 RKLHQRLQTTVIYVTHDQTEAMTMGDRIVVM--RDGVIQQ 216
            ++ ++L  T+++VTH   E++ + DRIVVM  R G I++
Sbjct: 178 LRIWEKLNKTILFVTHSIEESIYLADRIVVMTYRPGTIKR 217


Lambda     K      H
   0.321    0.138    0.395 

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: 238
Number of extensions: 9
Number of successful extensions: 2
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: 384
Length of database: 263
Length adjustment: 27
Effective length of query: 357
Effective length of database: 236
Effective search space:    84252
Effective search space used:    84252
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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