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 352308 BT2781 putative mannose-1-phosphate guanylyltransferase (NCBI ptt file)

Query= BRENDA::O58649
         (464 letters)



>FitnessBrowser__Btheta:352308
          Length = 360

 Score =  192 bits (489), Expect = 1e-53
 Identities = 120/350 (34%), Positives = 190/350 (54%), Gaps = 28/350 (8%)

Query: 4   LILAGGKGTRLWPLSREAMPKQFIKVF-SDRSLFQKTVERALIFSKPKEIFVVTNKEYRF 62
           +I+ GG G+R WP SR+ +PKQF+  F + RSL Q+T +R       + I +VTN  Y  
Sbjct: 9   VIMGGGIGSRFWPFSRKTLPKQFLDFFGTGRSLLQQTFDRFQKVIPTENILIVTNAMYAD 68

Query: 63  RVLDDLNELGLKVPEENILLEPVGKNTLPAIYWGLKVINDNYGDSVVAVLPSDHAIEVNE 122
            V + L EL     E+ ILLEP  +NT P I W    I     ++ + V PSDH I   E
Sbjct: 69  LVKEQLPELD----EKQILLEPARRNTAPCIAWAAYHIRALNPNANIVVAPSDHLILKEE 124

Query: 123 SYMEAFKKAEKLAE--KYLVTFGIKPTKPHTGYGYIKPGEKIEVEGKVLGYLVDEFKEKP 180
            +  A  K  +     + L+T GIKP +P TGYGYI+  E    +G    Y V  F EKP
Sbjct: 125 EFRAAIIKGLEFVSHSEKLLTLGIKPNRPETGYGYIQIDEPTG-DGF---YKVKTFTEKP 180

Query: 181 DLETARKYVENG-YYWNSGMFMFKVSVFMEEARKHSPDVVKAFEEGKSI----------E 229
           +LE A+ +VE+G +YWNSG+FM+ V+  ++ A    P++V     GK+I          E
Sbjct: 181 ELELAKVFVESGEFYWNSGLFMWNVNTIIKAAEILLPELVSKLAPGKNIYATDKEKAFIE 240

Query: 230 EIYELAPEISVDYGIMEKTNKAAVVPLNTYWNDLGSFDAVYEALEKDENGNAVHVTGFKA 289
           E +   P +S+D+GIMEK +   V   +  W+DLG++ ++Y+  E+D  GN       K+
Sbjct: 241 ENFPACPNVSIDFGIMEKADNVYVSLGDFGWSDLGTWGSLYDLSERDREGNVT----LKS 296

Query: 290 KYINVDSRNNLVLTE--RLTATVGVEDLVIIDTGDALLVAKRGETQKVKE 337
             +  + ++N+++    +L    G+E  +I ++ + LL+ ++ E   +++
Sbjct: 297 HSLIYNGKDNMIVLPKGKLAVIDGLEGYLIAESDNVLLICRKDEEHSIRK 346


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: 493
Number of extensions: 40
Number of successful extensions: 8
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: 360
Length adjustment: 31
Effective length of query: 433
Effective length of database: 329
Effective search space:   142457
Effective search space used:   142457
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