Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate AO353_02025 AO353_02025 mannose-1-phosphate guanyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__pseudo3_N2E3:AO353_02025 Length = 486 Score = 444 bits (1142), Expect = e-129 Identities = 233/476 (48%), Positives = 317/476 (66%), Gaps = 9/476 (1%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEH 59 +IPVILSGG GSRLWP+SR+ +PK F+ L G L Q+T R + +G+ L V N+E Sbjct: 3 LIPVILSGGVGSRLWPVSREAHPKPFMDLPGGQNLIQKTFLRASQLEGVVEVLTVTNREL 62 Query: 60 RFIVQEQLEAQNLA--SQAILLEPFGRNTAPAVAIAAMKLVA-EGRDELLLILPADHVIE 116 F +++ A N A SQ +LEPFGRNTA AVA AA++L A G + +L+L ADH+I+ Sbjct: 63 LFKTEDEYGAVNTAKHSQGFILEPFGRNTAAAVAAAALQLEATHGSNVHMLVLAADHLIK 122 Query: 117 DQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKP 176 D++AF A+A A A +G +V FGI + PETG+GYI A +A L G+ +V FVEKP Sbjct: 123 DEKAFAAAVANAVTLAAEGWLVTFGIQPTYPETGFGYIEAQKNAPLNGGL-KVARFVEKP 181 Query: 177 DEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGD----L 232 D A+ +V AG YYWNSGMF FR LEEL++H D+ + +E+S+ Sbjct: 182 DLETAQGYVGAGNYYWNSGMFCFRVGTVLEELREHAPDVVEAVARTIEQSRVTSSDKYRC 241 Query: 233 VNIDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKG 292 + +DA F PD SIDYA+ME++++ +P GW+D+GSW+++ ++ A DA+GN +G Sbjct: 242 LALDAEAFAEVPDISIDYALMERSAKVATIPCDIGWSDIGSWNAVAELTAPDADGNRFEG 301 Query: 293 DVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRS 352 +VL H S N V+ G+L +++G+ED++V++T DA+MIAHKD QDVKH+V L A + Sbjct: 302 EVLSHGSRNNYVNSEGRLTALVGVEDLLVIDTPDAVMIAHKDHAQDVKHIVGQLKANSHT 361 Query: 353 ETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTC 412 H V+RPWG+Y +++ G RF++K I VKP A LSLQMHHHR+EHWIVVSG A V Sbjct: 362 VHLLHRTVHRPWGTYTTLENGERFKIKRIVVKPKASLSLQMHHHRSEHWIVVSGMAVVIN 421 Query: 413 DDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 D + +L N+ST+I HRL NPG I L +IEVQSG YLGEDDI R ED YGR Sbjct: 422 DQQELMLNTNESTFIRAGHKHRLQNPGVIDLVMIEVQSGDYLGEDDIVRFEDNYGR 477 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: 636 Number of extensions: 30 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: 486 Length adjustment: 34 Effective length of query: 447 Effective length of database: 452 Effective search space: 202044 Effective search space used: 202044 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 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