Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_010961278.1 MCA_RS09945 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_000008325.1:WP_010961278.1 Length = 485 Score = 497 bits (1280), Expect = e-145 Identities = 252/480 (52%), Positives = 336/480 (70%), Gaps = 14/480 (2%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA------FDGMQAPLLVCN 56 P+ILSGG GSRLWP SR+ YPKQFL L G+ TLFQ+T R+ FD +++PL+VCN Sbjct: 8 PLILSGGVGSRLWPHSREAYPKQFLPLLGERTLFQETTGRIGGMAESRFD-IRSPLIVCN 66 Query: 57 KEHRFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAE-GRDELLLILPADHVI 115 ++HRF+V EQL ILLEP GRNTAPA+ IAA+ + G D +L ++PADH I Sbjct: 67 EQHRFLVAEQLRQMGYDDADILLEPSGRNTAPALTIAALHVSERLGGDCILAVMPADHHI 126 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEG-VSRVQSFVE 174 D F+ LA A A +G + FGI RPETGYGYIR L +G V +++FVE Sbjct: 127 ADVEGFRAGLARALGVAGRGLIGTFGIVPDRPETGYGYIRKGRS--LEDGTVFELEAFVE 184 Query: 175 KPDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVN 234 KPD A +++++G Y WNSG+F+ RA+ +LE + H DI ++C A E++ DG+ + Sbjct: 185 KPDAETAAQYLSSGDYLWNSGLFVLRANVWLERIGSHRPDILESCSAAYEKATADGNFIR 244 Query: 235 IDAATFECCPDNSIDYAVMEK---TSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTK 291 +D F CP +SIDYAVMEK T +A V+PL GW D+GSW+S+ +V +D +GNV + Sbjct: 245 VDRTDFLRCPSDSIDYAVMEKLNGTGQAVVIPLDVGWCDLGSWASLSEVKPRDEHGNVVE 304 Query: 292 GDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGR 351 GDV D+ N L++ + + ++ IG++D++VV+T DA+++AHK + QD+K + + L+A R Sbjct: 305 GDVYARDTRNSLLYADSRFLAAIGVDDLLVVDTADAVLVAHKSKAQDIKQIAEHLEAANR 364 Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVT 411 +E + H V+RPWG+Y+S+D G R+QVK ITV PGA LSLQMHHHRAEHWIVV GTA+V Sbjct: 365 TEHKVHRRVHRPWGTYESIDTGQRYQVKRITVTPGAALSLQMHHHRAEHWIVVRGTARVV 424 Query: 412 CDDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRTAE 471 +++FLLTENQSTYIPI HRL NPG IPLEIIEVQSGSYLGEDDI R +D Y RT E Sbjct: 425 RGEESFLLTENQSTYIPIGVHHRLENPGTIPLEIIEVQSGSYLGEDDIVRFQDHYHRTKE 484 Lambda K H 0.319 0.134 0.400 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: 680 Number of extensions: 44 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 481 Length of database: 485 Length adjustment: 34 Effective length of query: 447 Effective length of database: 451 Effective search space: 201597 Effective search space used: 201597 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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