Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate BPHYT_RS03980 BPHYT_RS03980 mannose-1-phosphate guanyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS03980 Length = 515 Score = 457 bits (1175), Expect = e-133 Identities = 236/488 (48%), Positives = 314/488 (64%), Gaps = 27/488 (5%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQA-------PLLVC 55 PVIL+GGSG+RLWP+SR+ YPKQ + + G D+L Q T +R+ DG A P++VC Sbjct: 31 PVILAGGSGTRLWPVSRENYPKQLIDVVGSDSLLQATARRM--DGFPAGWSVDVSPIIVC 88 Query: 56 NKEHRFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVI 115 +EHRF++ EQL +N +++EP R+TAPA+ +AA A+G D +L+++PADH I Sbjct: 89 GEEHRFVIAEQLH-ENGVDARLIVEPARRDTAPALTLAASLACADGGDAILVVMPADHSI 147 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175 D A Q AL LA AE+G + G+P +RP+TG+GYIR + L G + FVEK Sbjct: 148 ADVPALQAALELAARYAEQGSIATLGVPPTRPDTGFGYIRVGTE--LAGGGHAIDGFVEK 205 Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNI 235 P E A ++VAAG Y+WNSG+F+ RAS +L+ LK+ D++ C A + DG Sbjct: 206 PAEELAAKYVAAGMYWWNSGIFIVRASVWLDTLKRLQPDMHSACERAFTGGRLDGAYFRP 265 Query: 236 DAATFECCPDNSIDYAVMEK---------------TSRACVVPLSAGWNDVGSWSSIWDV 280 F P NSIDYAVME+ T VV L+AGW+D+GSW ++W Sbjct: 266 LVDAFLSAPANSIDYAVMERLTETAGSETPDKAPATPAGVVVGLNAGWSDLGSWDAVWAA 325 Query: 281 HAKDANGNVTKGDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVK 340 KDANGN +G V + + H G+LV+ +G ++VVVET DA+++ + VQDVK Sbjct: 326 MEKDANGNAGRGRVTFEGAVSSYAHSEGRLVACVGTTNVVVVETADAVLVVDRSHVQDVK 385 Query: 341 HVVKDLDAQGRSETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEH 400 +V + AQ E H +V RPWG YDS+D G RFQVK I V PGA+LSLQ+HHHRAEH Sbjct: 386 GLVSRIKAQHAPEADAHRKVRRPWGFYDSIDHGERFQVKRIVVTPGAQLSLQLHHHRAEH 445 Query: 401 WIVVSGTAQVTCDDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIE 460 W+VV GTA VT ++ FLL+EN+STYIP+ HRL NPGK+PLEIIE+QSG+YLGEDDI Sbjct: 446 WVVVRGTALVTRGEEQFLLSENESTYIPLGIKHRLENPGKVPLEIIEIQSGAYLGEDDIV 505 Query: 461 RLEDVYGR 468 R D YGR Sbjct: 506 RFNDNYGR 513 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: 686 Number of extensions: 34 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: 515 Length adjustment: 34 Effective length of query: 447 Effective length of database: 481 Effective search space: 215007 Effective search space used: 215007 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