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 WP_007473673.1 CMTB2_RS02385 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::O58649 (464 letters) >NCBI__GCF_000170735.1:WP_007473673.1 Length = 462 Score = 438 bits (1127), Expect = e-127 Identities = 235/479 (49%), Positives = 318/479 (66%), Gaps = 33/479 (6%) Query: 1 MKALILAGGKGTRLWPLSREAMPKQFIKVFSDRSLFQKTVERALIFSKPKEIFVVTNKEY 60 M +IL GG GTRLWP+SRE +PKQF+K ++SLFQ T++R +SK + +V+N+ Sbjct: 1 MTNVILCGGSGTRLWPISRENLPKQFLKFIDNKSLFQLTLKRNSEYSK--DFLIVSNENQ 58 Query: 61 RFRVLDDLNELGLKVPEENILLEPVGKNTLPAIYWGLKVINDNYGDSVVAVLPSDHAIEV 120 F LD L E+G + ++EPVG+NT +I + ++ D ++ + PSDH IE Sbjct: 59 YFIALDQLEEMGFS--DSKFIIEPVGRNTAASIAFAAFSVDK---DEILFITPSDHLIEN 113 Query: 121 NESYMEAFKKAEKLAEK-YLVTFGIKPTKPHTGYGYIKPGEKIEVEGKVLGYLVDEFKEK 179 +E+Y +A + A+K A+ Y+VTFG+ P P TGYGYIK + K L V+ FKEK Sbjct: 114 DENYKKAIENAKKCAKDGYIVTFGVVPNSPKTGYGYIKA-----ISCKDLICDVESFKEK 168 Query: 180 PDLETARKYVENG-YYWNSGMFMFKVSVFMEEARKHSPDVV----KAFEEGKSIE----- 229 PD++TA+KY+E+G YYWNSGMFMFK V++ E +K++PD+ KA+E K E Sbjct: 169 PDIKTAKKYIEDGNYYWNSGMFMFKAEVYLNELKKYAPDIYEASKKAYENAKKGEFVRIK 228 Query: 230 --EIYELAPEISVDYGIMEKTNKAAVVPLNTYWNDLGSFDAVYEALEKDENGNAVHVTGF 287 ++ E+ E S+DY +ME + ++ N W D+G FDA+YE L KDENGN + Sbjct: 229 KDDMLEIRDE-SIDYAVMEHSKIIKMIKSNIKWQDVGDFDALYEVLPKDENGNTKN---- 283 Query: 288 KAKYINVDSRNNLVLTERLTATV--GVEDLVIIDTGDALLVAKRGETQKVKEVYKKLKEE 345 K + ++S+NNLV V + DL+I+DT ALLV KRG+ QKVKE+ K LKE+ Sbjct: 284 -DKLLALNSKNNLVFGRYKKQIVINDINDLIIVDTPTALLVTKRGDAQKVKEIVKILKEK 342 Query: 346 NDERAIVHRTAYRPWGSYTVLEEGERYKIKRLTVLPGKRLSLQIHYHRSEHWVVVRGTAK 405 N + RT YRPWG YT +EEG+ YK+K + V PGKRLSLQ H+HRSEHWVVV GTAK Sbjct: 343 NPDVVKFGRTVYRPWGKYTNIEEGDGYKVKLIVVNPGKRLSLQKHFHRSEHWVVVSGTAK 402 Query: 406 VKVGDKEFILRPGESTFIPAGVPHRLENPGKVILEVIETQIGEYLGEDDIVRLQDDYGR 464 V GDKEFILRP EST+IP G HRLENPGK+ L+++E Q+GEYL EDDIVR++DD+ R Sbjct: 403 VINGDKEFILRPNESTYIPMGEIHRLENPGKIPLKIVEVQVGEYLEEDDIVRIEDDFER 461 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: 673 Number of extensions: 33 Number of successful extensions: 9 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: 462 Length adjustment: 33 Effective length of query: 431 Effective length of database: 429 Effective search space: 184899 Effective search space used: 184899 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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