Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_084457146.1 G494_RS0120230 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_000429965.1:WP_084457146.1 Length = 469 Score = 464 bits (1193), Expect = e-135 Identities = 241/472 (51%), Positives = 314/472 (66%), Gaps = 10/472 (2%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEHRF 61 P+IL+GG+GSRLWPLSR+ YPKQ ++LTG+ +L Q TIKR+A + +AP++V +EHRF Sbjct: 5 PIILAGGTGSRLWPLSRELYPKQVISLTGELSLLQTTIKRVAELEHARAPIVVVGEEHRF 64 Query: 62 IVQEQLEAQNLASQ-AILLEPFGRNTAPAVAIAAMKLVAEGRDE-LLLILPADHVIEDQR 119 + + QLE L ILLEP G+NTAPA+ AA + +G E LL+LPADH+I Sbjct: 65 MTKSQLEELELFKDFQILLEPMGKNTAPAICGAAAFVARQGHGEDTLLVLPADHLITRPE 124 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 F QA+ A AE+G +V FGI PETGYGYI EG +V+ FVEKPD Sbjct: 125 IFAQAVERAVALAEQGMLVTFGIVPDHPETGYGYIAKG------EG-GKVERFVEKPDLV 177 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A+ ++ GGY WNSGMF F A L E++ + ++ + A+E+ + DG + Sbjct: 178 TAQAYLTQGGYLWNSGMFTFSAQTLLAEMQLYAPEVVECMAEAVEQGRFDGVFFRFNREI 237 Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299 CP +SIDYA+MEKT A VV GW+D+GSW ++W+V KD GNV GDVL+ D Sbjct: 238 MASCPSDSIDYALMEKTRNAAVVEADIGWSDIGSWQALWEVADKDERGNVAGGDVLLEDV 297 Query: 300 HNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCE 359 N LV LV+ +GL++ +V+ET DA+++A DR QDVK +V L + R E Q H Sbjct: 298 ENSLVRSEHTLVAAVGLKNTMVIETADAVLVAPMDRSQDVKKIVTRLKREKRGEFQVHKT 357 Query: 360 VYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLL 419 VYRPWGSY +++M RFQ+K ITV PGA+LSLQMHHHR EHW+VVSGTA+V +++ LL Sbjct: 358 VYRPWGSYTTLEMQDRFQIKRITVNPGAKLSLQMHHHRHEHWVVVSGTARVVNGEESILL 417 Query: 420 TENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRTAE 471 E+QSTYIP + HRL NPG IPLE+IEVQ GSYLGEDDI R +D YGR E Sbjct: 418 QEDQSTYIPSGTRHRLENPGVIPLELIEVQIGSYLGEDDIVRFDDDYGRQEE 469 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: 631 Number of extensions: 22 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: 469 Length adjustment: 33 Effective length of query: 448 Effective length of database: 436 Effective search space: 195328 Effective search space used: 195328 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 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