Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate N515DRAFT_4299 N515DRAFT_4299 mannose-1-phosphate guanylyltransferase / mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Dyella79:N515DRAFT_4299 Length = 470 Score = 509 bits (1312), Expect = e-149 Identities = 256/471 (54%), Positives = 333/471 (70%), Gaps = 4/471 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAF-DGMQAPLLVCNKEH 59 +IP++LSGGSG+RLWP+SRK PKQFL+L G TLFQQT+ R + +P++V +++H Sbjct: 2 LIPLVLSGGSGTRLWPVSRKNLPKQFLSLMGQGTLFQQTVARTRLLPDVASPIVVASEDH 61 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RF+V EQL + I+LEP RNTAPA+A+ A++ V + + LLL+LPADH+I D+ Sbjct: 62 RFLVAEQLLESGIQDATIVLEPLPRNTAPAIALGALQAVGQDPEALLLVLPADHLIGDED 121 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 +F+ A+ A AA +V FGI RPETG+GYIR DA + +V FVEKP Sbjct: 122 SFRDAVEQALPAARDNWLVTFGIRPDRPETGFGYIRRG-DA-IGGHAYKVAEFVEKPALE 179 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A+ ++ GGY WNSGMFLF+A+R+L+EL H + A ++ D D V +DA Sbjct: 180 TAQGYIEHGGYDWNSGMFLFKAARFLDELAAHAPAMLQAVRAAHASAKADLDFVRVDADA 239 Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299 F P+NSIDYAVMEKT A V+P+S W+D+GSWS++W +DA N+ +GD + + Sbjct: 240 FAQVPENSIDYAVMEKTRHAAVIPVSCAWSDIGSWSALWLAGVRDAQDNLREGDTIAIKT 299 Query: 300 HNCLVHGNGK-LVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358 H L+ + + L++ +G++D++VV T DA ++AH+D QDVK VV +L A GR+E H Sbjct: 300 HRSLLRSHDRHLLATVGVDDLIVVTTPDATLVAHRDAAQDVKRVVDELKAAGRTEHSLHR 359 Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418 V RPWGSYDS++ RFQVK I VKPGA LSLQ HHHRAEHWIVVSGTA+VTCDDK FL Sbjct: 360 VVRRPWGSYDSLESADRFQVKRIVVKPGAALSLQKHHHRAEHWIVVSGTAEVTCDDKVFL 419 Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 L ENQSTYIP+ SVHRL NPGK+PLEIIEVQSGSYLGEDDI RLEDVYGR+ Sbjct: 420 LGENQSTYIPLGSVHRLRNPGKVPLEIIEVQSGSYLGEDDIVRLEDVYGRS 470 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: 29 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: 470 Length adjustment: 33 Effective length of query: 448 Effective length of database: 437 Effective search space: 195776 Effective search space used: 195776 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