GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Halomonas xinjiangensis TRM 0175

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  313 bits (801), Expect = 6e-90
 Identities = 172/356 (48%), Positives = 236/356 (66%), Gaps = 17/356 (4%)

Query: 1   MADLKLTGVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59
           MA ++LTG++K Y G+V+ +  I+L+I  GE +V VGPSGCGKSTLLRM+AGLE IT GT
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           L+ID  VVND+ PA+R IAMVFQ+YALYPHMTV  N+++ LK     + EI+  V  AA 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            L++  +L+R P+ LSGGQRQRVA+GR++VR+P  +LFDEPLSNLDA LRV  R+EI QL
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
           +  + ++T +YVTHDQ+EA+TL  R+VVL GG I QVG+P+E+YEKP + FVA FIGSP 
Sbjct: 181 QRRL-KTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239

Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDY-V 298
           MN+LP   +            G   + D+ + D+ +     +G+RP+D+   AP  D+ V
Sbjct: 240 MNMLPVAYL---------RERGANGLLDHLAADTDV-----IGIRPDDLRIEAPDEDHLV 285

Query: 299 FEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
             G V + EA G  + LY      + PT+ +        +G+  R    P+ +H F
Sbjct: 286 VTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPF 341


Lambda     K      H
   0.316    0.135    0.379 

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: 379
Number of extensions: 19
Number of successful extensions: 5
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: 373
Length of database: 354
Length adjustment: 29
Effective length of query: 344
Effective length of database: 325
Effective search space:   111800
Effective search space used:   111800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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