GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS19200 CA265_RS19200 mannose-1-phosphate guanylyltransferase

Query= BRENDA::O58649
         (464 letters)



>FitnessBrowser__Pedo557:CA265_RS19200
          Length = 349

 Score =  199 bits (506), Expect = 1e-55
 Identities = 121/350 (34%), Positives = 186/350 (53%), Gaps = 31/350 (8%)

Query: 6   LAGGKGTRLWPLSREAMPKQFIKVFS-DRSLFQKTVERALIFSKPKEIFVVTNKEYRFRV 64
           +AGG G+R WP SR   PKQFI +    +SL Q T ER L     ++I+++TN+ Y   V
Sbjct: 1   MAGGVGSRFWPKSRNHFPKQFIDILGLGKSLLQLTYERFLNICPKEQIYILTNESYSGLV 60

Query: 65  LDDLNELGLKVPEENILLEPVGKNTLPAIYWGLKVINDNYGDSVVAVLPSDHAIEVNESY 124
            D L  L       NILLEP   NT P I +    I     D+ + V PSDH I   + +
Sbjct: 61  ADQLPNL----LANNILLEPSRNNTAPCIAYASYKIFQINPDANIVVAPSDHLILKEQEF 116

Query: 125 MEAFKKAEKLAEKY--LVTFGIKPTKPHTGYGYIKPGEKIEVEGKVLGYLVDEFKEKPDL 182
           +    +A   A ++  L+T GI PT+P TGYGYI+  + +    KV     + F EKP L
Sbjct: 117 LTKVDQALTFAAEHDALLTLGISPTRPDTGYGYIRYQDGLSEVKKV-----EAFMEKPSL 171

Query: 183 ETARKYVENG-YYWNSGMFMFKVSVFMEEARKHSPDVVKAF----------EEGKSIEEI 231
           E A +Y+ NG Y WN+G+F++ V    +   K++ D+ K F          EE   I E 
Sbjct: 172 EKAEEYLANGDYVWNAGIFIWSVKAIKKAFNKYATDIDKIFTRGDNFYNTKEETNYIIEN 231

Query: 232 YELAPEISVDYGIMEKTNKAAVVPLNTYWNDLGSFDAVYEALEKDENGNAVHVTGFKAKY 291
           Y  AP IS+DY I+EK +    +P +  W+DLG++ +++    KD N NAV+       +
Sbjct: 232 YPTAPNISIDYAILEKADNVYTIPADIGWSDLGTWASLHTVANKDVNANAVN-----CAF 286

Query: 292 INVDSRNNLVL---TERLTATVGVEDLVIIDTGDALLVAKRGETQKVKEV 338
           +++D  +N ++     +     G+E+ +I+D G  LL+  + + Q++K+V
Sbjct: 287 LHLDKTSNCIIQLPDNKAAVIKGMENYIIVDDGKVLLIYPKSDEQEIKQV 336


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: 399
Number of extensions: 22
Number of successful extensions: 7
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: 349
Length adjustment: 31
Effective length of query: 433
Effective length of database: 318
Effective search space:   137694
Effective search space used:   137694
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