GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Caldicellulosiruptor kronotskyensis 2002

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_013429918.1 CALKRO_RS04565 cell division ATP-binding protein FtsE

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000166775.1:WP_013429918.1
          Length = 239

 Score =  123 bits (309), Expect = 5e-33
 Identities = 75/223 (33%), Positives = 124/223 (55%), Gaps = 8/223 (3%)

Query: 8   HIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDR 67
           ++ K YP      + + NL I+  EF   VG SG GK+T ++++    D TEG + +G+ 
Sbjct: 6   NVSKRYPNGVL-ALTNINLTIEKGEFVFLVGSSGAGKSTIVKLLLKEIDPTEGEIIVGEY 64

Query: 68  RVNDVPPKD-----RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKI 122
           ++  +P ++     R I +VFQ++ L P+ TVY+N+ F +++   P   I R+V     +
Sbjct: 65  KLTQLPKREIPYYRRKIGIVFQDFRLLPNKTVYENVEFAMQITGAPAKIIRRQVPYVLSL 124

Query: 123 LDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLH 182
           + +AH     P  LSGG++QRVAL RAIV +P + + DEP  NLD     ++   +  ++
Sbjct: 125 VGLAHKAKCYPHELSGGEQQRVALARAIVNKPNLLVADEPTGNLDPDTSWEIMRLLEDIN 184

Query: 183 QRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYS 225
           +R  TTV+  TH +    +M  R+V +  G I + D  + VYS
Sbjct: 185 KR-GTTVLVATHAKEIVDSMRKRVVAIDCGRIVK-DQHRGVYS 225


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: 195
Number of extensions: 8
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: 239
Length adjustment: 27
Effective length of query: 357
Effective length of database: 212
Effective search space:    75684
Effective search space used:    75684
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 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