Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate BPHYT_RS31080 BPHYT_RS31080 mannose-1-phosphate guanyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS31080 Length = 477 Score = 457 bits (1176), Expect = e-133 Identities = 234/472 (49%), Positives = 312/472 (66%), Gaps = 3/472 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPLLVCNKEH 59 + PV+L GGSG+RLWP+SR PKQFL L G+ +L Q T++R+ A D + P+LV N E+ Sbjct: 3 IFPVVLCGGSGTRLWPMSRGGQPKQFLTLAGEHSLLQTTLRRVNALDNTRPPVLVSNAEY 62 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RF + +QL+ L AI+LEP RNTA A+A AA + + LLL+LP+DHVI++ Sbjct: 63 RFQLADQLKEIALDVSAIILEPVSRNTAAAIAAAAHFAIQDDPKALLLVLPSDHVIQNAD 122 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASAD-AQLPEGVSRVQSFVEKPDE 178 AF A+ A G +V FG+ + P TG+GYIR A V +FVEKPD Sbjct: 123 AFHNAVETGIALARDGRLVTFGVVPTTPHTGFGYIRKGESLADKEHEAYNVSAFVEKPDA 182 Query: 179 ARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAA 238 A A E +A+G Y WNSG+FLF A YL+ELK+++ D+ A + + D + + Sbjct: 183 ALAAELLASGDYLWNSGIFLFGAGVYLDELKRYEPDVARFADQAYKDAHPDLQFLRLGKD 242 Query: 239 TFECCPDNSIDYAVMEKTSRACVVPLS-AGWNDVGSWSSIWDVHAKDANGNVTKGDVLVH 297 F CP S+DYAV+E+T RA V+ + GW+D+GSWS++ ++ D N GDVL Sbjct: 243 AFTDCPSISVDYAVLERTDRAAVISVDDLGWSDIGSWSALHEIAPHDEQRNALIGDVLQD 302 Query: 298 DSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNH 357 N + ++V+ IG+ D+++VET DA+++AH+D ++VK +V L+A GR E+ H Sbjct: 303 SVSNSYIRAEHRMVAAIGVSDLIIVETADAVLVAHRDLAKNVKTIVDSLNATGRRESVTH 362 Query: 358 CEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTF 417 V RPWGSY+S+D G RFQVK I V PGA+LSLQ+HHHRAEHWIVV GTA VT ++ Sbjct: 363 RRVTRPWGSYESIDQGERFQVKRIVVNPGAQLSLQLHHHRAEHWIVVRGTALVTNGERED 422 Query: 418 LLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 LLTENQSTYIP+ HRL NPGKIPLE+IEVQSG+YLGEDDI RLED YGRT Sbjct: 423 LLTENQSTYIPVGVSHRLFNPGKIPLELIEVQSGAYLGEDDIVRLEDRYGRT 474 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: 584 Number of extensions: 21 Number of successful extensions: 4 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: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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: 51 (24.3 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