GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcU in Acidovorax sp. GW101-3H11

Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate Ac3H11_2065 Maltose/maltodextrin ABC transporter, permease protein MalG

Query= TCDB::Q97UY9
         (287 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2065
          Length = 289

 Score =  132 bits (332), Expect = 9e-36
 Identities = 85/290 (29%), Positives = 142/290 (48%), Gaps = 19/290 (6%)

Query: 7   PVIKASLHYLALAIVSVIWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLLS 66
           P +   L Y  LA+ +  +L+P+YAML+  FK   E+ ST +L  P  + + A+ +   S
Sbjct: 9   PSVGRFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWSAWGTAWQS 68

Query: 67  ---------LAKPLINSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAISDVLFSL 117
                    L    +NS+ + +P   IS   GA+  Y      +  S       D LF +
Sbjct: 69  ACTGVDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGS-------DALFGM 121

Query: 118 ISLATFIPQEATLLPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISVIPRSLI 177
           +    F+P +  LLP+++++  +GL  S  G++    +  +    L    + + IP+ L+
Sbjct: 122 LLFGVFMPFQVVLLPMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELV 181

Query: 178 EAAKMDGTGDLKIFMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMKLT-SIA 236
            AA+MDG    +IF +IV PLS P  + TLI+     WN+F   +V   T    +T  + 
Sbjct: 182 NAARMDGASFFQIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVFSGTDSKPVTVGLN 241

Query: 237 VLSYSGAYGTLYNDTFAAGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286
            L+ + +    YN   AA ++A +  + I+V  G++F+RGL A  G  KG
Sbjct: 242 NLANTSSSVKAYNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTA--GAVKG 289


Lambda     K      H
   0.330    0.144    0.417 

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: 227
Number of extensions: 15
Number of successful extensions: 4
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: 287
Length of database: 289
Length adjustment: 26
Effective length of query: 261
Effective length of database: 263
Effective search space:    68643
Effective search space used:    68643
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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