GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Hydrogenovibrio kuenenii DSM 12350

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000526715.1:WP_024851725.1
          Length = 282

 Score =  145 bits (367), Expect = 1e-39
 Identities = 87/217 (40%), Positives = 131/217 (60%), Gaps = 14/217 (6%)

Query: 3   RVLLEHIYKTY---PGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITE 59
           ++++  + KT+    G  E  ++  +L +++ EF   VG SGCGK+T LR+I GLE +T+
Sbjct: 4   KIIISGLNKTFITKKGAVE-VLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTK 62

Query: 60  GNLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKA----EIDRR 115
           G + + +  VN  P KDR  AMVFQ+Y+LYP +TV +N+ F   L+   +     +I   
Sbjct: 63  GQVLVDEEIVNK-PGKDR--AMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSM 119

Query: 116 VQEAAKILDIAHL---LDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRV 172
           V  +  +LD+  L    D  P  LSGG RQRVA+ RA++ +P V LMDEP   LDA+ R 
Sbjct: 120 VDRSYALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTRE 179

Query: 173 QMRAEIRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVM 209
            M   I  L +  ++T+++VTHD  EA+ + DR+VVM
Sbjct: 180 VMHDLILHLFEIEKSTIVFVTHDVEEAIYLADRVVVM 216


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: 258
Number of extensions: 8
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: 384
Length of database: 282
Length adjustment: 28
Effective length of query: 356
Effective length of database: 254
Effective search space:    90424
Effective search space used:    90424
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 Apr 09 2024. 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