Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_011765816.1 AZO_RS10530 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_000061505.1:WP_011765816.1 Length = 482 Score = 512 bits (1319), Expect = e-150 Identities = 263/476 (55%), Positives = 328/476 (68%), Gaps = 11/476 (2%) Query: 4 VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL---AFDGMQAPLLVCNKEHR 60 VILSGGSG+RLWP SR+ YPKQ L LTG+ +L Q+T RL A + PL+V N+++R Sbjct: 6 VILSGGSGTRLWPASRETYPKQLLPLTGELSLLQETAVRLKDFAGEVDPVPLVVTNEDYR 65 Query: 61 FIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRA 120 FI+ EQL +AS I+LEP GRNTAPA+ +AA+ A G D +LL++PADHVI D Sbjct: 66 FIIAEQLRQIGVASAGIVLEPVGRNTAPALTLAALAAAAGGNDPVLLVMPADHVITDVER 125 Query: 121 FQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQS-FVEKPDEA 179 FQ A+ A G +V FGI PETGYGYIR A SRV + FVEKPD Sbjct: 126 FQLAIGEGAALASAGALVTFGIVPDHPETGYGYIRVGP-AVSGAATSRVLAEFVEKPDAP 184 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A +VA+G Y+WNSG+F+ +AS +L +++ + ++ C A + D D + + Sbjct: 185 TAERYVASGEYFWNSGIFMMKASVWLRAIERFNPEMAAACEAAFVERKADADFLRVGKGA 244 Query: 240 FECCPDNSIDYAVMEKTSRA------CVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGD 293 FE CP +SIDYAVMEK A VVPLSAGW+DVG+W ++W V KDA+GN +G+ Sbjct: 245 FENCPSDSIDYAVMEKLQSAPEVGQGVVVPLSAGWSDVGAWDALWAVSPKDASGNSARGE 304 Query: 294 VLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSE 353 VL S N LVH + +LV+ +G +D+VVVET DA+M+AHK Q VK+VV L A+GRS Sbjct: 305 VLFESSRNTLVHASTRLVAAVGCDDMVVVETADAVMVAHKSHTQSVKNVVARLKAEGRSL 364 Query: 354 TQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCD 413 T+ H +VYRPWG YDS+D G RFQVK I V PGA+LSLQMH+HRAEHWIVV GTA+VT Sbjct: 365 TRTHRKVYRPWGWYDSIDAGDRFQVKRIVVNPGAKLSLQMHYHRAEHWIVVRGTAEVTAG 424 Query: 414 DKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 DK FLL EN+STYIP+ HRL NPGK+PLEIIEVQSGSYLGEDDI R ED YGRT Sbjct: 425 DKVFLLGENESTYIPLGHTHRLTNPGKVPLEIIEVQSGSYLGEDDIVRFEDTYGRT 480 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: 618 Number of extensions: 28 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: 482 Length adjustment: 34 Effective length of query: 447 Effective length of database: 448 Effective search space: 200256 Effective search space used: 200256 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