Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate RR42_RS34480 RR42_RS34480 mannose-1-phosphate guanyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Cup4G11:RR42_RS34480 Length = 492 Score = 477 bits (1228), Expect = e-139 Identities = 234/483 (48%), Positives = 328/483 (67%), Gaps = 18/483 (3%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQA-------PLLVC 55 PV+L+GG+G+RLWPLSR+ +PKQ + L G D+L Q T+ R+ G A ++VC Sbjct: 13 PVVLAGGAGTRLWPLSREHFPKQLIDLVGKDSLLQSTLLRM--QGFSAGHEIEPSAIIVC 70 Query: 56 NKEHRFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVI 115 EHRFI EQL+A + + +++EP RNTAPA+ +AA +A+G+D +L+++PADH I Sbjct: 71 GDEHRFITSEQLQASGMQGR-LVVEPVRRNTAPALTLAASLALADGQDAILVVMPADHAI 129 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175 D AF QAL++A A +G +V G+P +RP+TGYGYI+ LP+GV R++ FVEK Sbjct: 130 PDTCAFHQALSIAAAHASEGAIVTLGVPPTRPDTGYGYIKLGE--MLPDGVRRMERFVEK 187 Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNI 235 P A ++VA+G Y+WNSG+F+ RA+ +++ ++ I++ C+ ++ + +G Sbjct: 188 PAIELAAQYVASGNYWWNSGIFVVRATVWMQAIEALHPAIHEMCVASVAEGKQEGQFFRP 247 Query: 236 DAATFECCPDNSIDYAVMEKTS------RACVVPLSAGWNDVGSWSSIWDVHAKDANGNV 289 + F P +SIDYAVME+ R VVPL AGW+D+GSW ++WD KDA GN Sbjct: 248 ASRQFFLSPSDSIDYAVMERLDNPASPCRGVVVPLEAGWSDLGSWDAVWDAMDKDAEGNA 307 Query: 290 TKGDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQ 349 +G V+ +H+ VH +G+LV+ +G +IVVVET DA+++ + VQDVK VV + Sbjct: 308 GRGRVVFEGAHSSYVHSDGRLVACVGTSNIVVVETADAVLVVDRSHVQDVKDVVARMKIL 367 Query: 350 GRSETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQ 409 E H +V RPWG YDS++ G RFQVK I V+PGARLSLQ+HHHRAEHW+VVSGTA Sbjct: 368 HAPEADTHRKVRRPWGFYDSIEHGDRFQVKRIVVQPGARLSLQLHHHRAEHWVVVSGTAM 427 Query: 410 VTCDDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 VT ++ FLL+ENQST+IP+ +HRL NPGK+PLEIIE+QSG YLGEDDI R++D YGR Sbjct: 428 VTRGEEQFLLSENQSTFIPLGVLHRLENPGKLPLEIIEIQSGGYLGEDDIVRVDDTYGRC 487 Query: 470 AEP 472 P Sbjct: 488 PGP 490 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: 697 Number of extensions: 30 Number of successful extensions: 5 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: 481 Length of database: 492 Length adjustment: 34 Effective length of query: 447 Effective length of database: 458 Effective search space: 204726 Effective search space used: 204726 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 17 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