Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate AO353_10250 AO353_10250 mannose-1-phosphate guanylyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10250 Length = 480 Score = 377 bits (968), Expect = e-109 Identities = 204/478 (42%), Positives = 294/478 (61%), Gaps = 11/478 (2%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLL-VCNKE 58 +IPVILSGG+G+RLWP+SR+ +PK F+ L TL +T +R A G ++ V N++ Sbjct: 2 LIPVILSGGAGTRLWPVSREGHPKPFMTLPDGQTLLGKTYQRAAGLLGTHGDIVTVTNRD 61 Query: 59 HRFIVQEQLEAQNLASQA--ILLEPFGRNTAPAVAIAAMKLVA-EGRDELLLILPADHVI 115 + F ++ + +L +LEP GRNTAPA+A AA+ L A G + +L+++PADH+I Sbjct: 62 YYFQSKDHYQDAHLGHHRGHFVLEPVGRNTAPAIAAAALSLQALHGNEAILVVMPADHLI 121 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175 +++ AF+ A+ A AE G +V FG+ + PETG+GYI +G ++V FVEK Sbjct: 122 QNEDAFKTAVRHAVKLAEAGHLVTFGVIPTAPETGFGYIERGEPLD-EQGATKVARFVEK 180 Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIY---DTCLLALERSQHDGDL 232 PD A ++ +G + WNSGMF F L +L+ H + D CL A + G L Sbjct: 181 PDLQTAMHYLESGNFLWNSGMFCFSVGTLLAQLQLHAPQLLEQADACLAASTTVETGGCL 240 Query: 233 VN-IDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTK 291 + A F D SIDYA+ME++++ V+P + +GSW ++ + A DA N Sbjct: 241 QQELSATHFAEMTDISIDYALMERSNKVVVIPAGFDCSGIGSWGAVSALVAADAQNNRAS 300 Query: 292 GDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGR 351 GD L DSHN V +G++V+ +G+++++V++T DA+++AH DR QDV+ VVK L + Sbjct: 301 GDALFIDSHNNFVQSDGRMVATVGVDNLIVIDTADAVLVAHTDRAQDVRKVVKQLKEKEH 360 Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVT 411 H V RPWG+Y ++ G RF++K I VK GA+LSLQMHHHR EHW+ G A+VT Sbjct: 361 ESYSLHRTVSRPWGTYTVLEEGPRFKIKRIVVKSGAKLSLQMHHHRNEHWVEAEGMAKVT 420 Query: 412 CDDK-TFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 + + L+ +N+ST+I HRL NPG I L IIEVQSG YLGEDDI R ED YGR Sbjct: 421 NNGSGSRLVAKNESTFIAAGHKHRLENPGVIDLVIIEVQSGEYLGEDDIVRFEDQYGR 478 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: 582 Number of extensions: 32 Number of successful extensions: 6 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: 480 Length adjustment: 34 Effective length of query: 447 Effective length of database: 446 Effective search space: 199362 Effective search space used: 199362 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