GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Bacteroides thetaiotaomicron VPI-5482

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13); glucose-1-phosphate guanylyltransferase (EC 2.7.7.34); aldose-1-phosphate nucleotidyltransferase (EC 2.7.7.37); mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate 350086 BT0558 mannose-1-phosphate guanylyltransferase (NCBI ptt file)

Query= BRENDA::O58649
         (464 letters)



>FitnessBrowser__Btheta:350086
          Length = 350

 Score =  199 bits (506), Expect = 1e-55
 Identities = 120/353 (33%), Positives = 196/353 (55%), Gaps = 26/353 (7%)

Query: 4   LILAGGKGTRLWPLSREAMPKQFIKVFS-DRSLFQKTVERALIFSKPKEIFVVTNKEYRF 62
           +I+AGG G+R WP+S    PKQFI V    R+L Q T +R       + ++VVT+++Y  
Sbjct: 8   VIMAGGIGSRFWPMSTPECPKQFIDVMGCGRTLIQLTADRFDGVCPRENVWVVTSEKY-- 65

Query: 63  RVLDDLNELGLKVPEENILLEPVGKNTLPAIYWGLKVINDNYGDSVVAVLPSDHAIEVNE 122
             +D + E   ++PE NIL EP  +NT P I +    I   + ++ V V PSD  +    
Sbjct: 66  --IDIVREQLPEIPESNILAEPCARNTAPCIAYACWKIKKKHPNANVVVTPSDALVINTG 123

Query: 123 SYMEAFKKAEKLAEKY--LVTFGIKPTKPHTGYGYIKPGEKIEVEGKVLGYLVDEFKEKP 180
            +    +KA +  +    +VT GIKPT+P TGYGYI  G++I  + ++  + VD FKEKP
Sbjct: 124 EFRRVVEKALRFTDNSSAIVTLGIKPTRPETGYGYIAAGDQIMTDKEI--FTVDAFKEKP 181

Query: 181 DLETARKYVENG-YYWNSGMFMFKVSVFMEEARKHSPDVVKAFE----------EGKSIE 229
           D ETA +Y+  G Y+WN+G+F++ V       R ++P + + F+          E ++I+
Sbjct: 182 DRETADRYLAEGNYFWNAGIFVWNVRTITSVMRVYAPGIAQIFDRIFPDFYTEKENETIK 241

Query: 230 EIYELAPEISVDYGIMEKTNKAAVVPLNTYWNDLGSFDAVYEALEKDENGNAVHVTGFKA 289
           +++     IS+DY +MEK  +  V+P +  W+DLG++ A+   L +D++GNA       A
Sbjct: 242 KLFPTCEAISIDYAVMEKAQEIYVLPASFGWSDLGTWGALRGLLPQDKSGNAT----VGA 297

Query: 290 KYINVDSRNNLVLT--ERLTATVGVEDLVIIDTGDALLVAKRGETQKVKEVYK 340
                +S+N +V T  E+     G++  +I +  + LL+ K  E Q++KE  K
Sbjct: 298 DVRLYESKNCIVHTSEEKRVVIQGLDGYIIAEKDNTLLICKLDEEQRIKEFSK 350


Lambda     K      H
   0.316    0.137    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: 388
Number of extensions: 19
Number of successful extensions: 6
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: 464
Length of database: 350
Length adjustment: 31
Effective length of query: 433
Effective length of database: 319
Effective search space:   138127
Effective search space used:   138127
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: 50 (23.9 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