Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate PP_1776 PP_1776 Mannose-6-phosphate isomerase/mannose-1-phosphate guanylyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Putida:PP_1776 Length = 480 Score = 424 bits (1090), Expect = e-123 Identities = 223/477 (46%), Positives = 311/477 (65%), Gaps = 11/477 (2%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEH 59 +IPVILSGG GSRLWP+SR+ +PK F+ L L Q+T R A +G+ L V N+E Sbjct: 3 LIPVILSGGVGSRLWPVSREAHPKPFMTLPDGQNLIQKTFLRAADLNGVVEILTVTNREL 62 Query: 60 RFIVQEQ---LEAQNLASQAILLEPFGRNTAPAVAIAAMKLV-AEGRDELLLILPADHVI 115 F +++ + QNL SQ +LEPFGRNTA AVA AA++L+ + G +L+L ADH+I Sbjct: 63 LFKTEDEYRTINKQNL-SQGYILEPFGRNTAAAVAAAALQLLESHGPQVHMLVLAADHLI 121 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175 +++ AF +A++ A A +G +V FGI PETG+GYI A+A L EG RV+ FVEK Sbjct: 122 QNEAAFSEAVSKAVQLAGEGWLVTFGIKPQYPETGFGYIEAAAGGVL-EGGLRVERFVEK 180 Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGD---- 231 PD A +VAAG Y+WN+GMF F+ +E+ + + D+ + LE S+ Sbjct: 181 PDAKTAEAYVAAGNYFWNAGMFCFQVGTVIEQFRAYAPDVLEAVERTLEASRRSTSKGYS 240 Query: 232 LVNIDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTK 291 + +DA F PD SIDYA+ME++S+ +P GW+D+GSW+++ ++ D +GN Sbjct: 241 CLALDAECFASVPDISIDYALMERSSKVATIPCDIGWSDIGSWNAVSELTLPDEHGNRFD 300 Query: 292 GDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGR 351 G+V+ + + N V +L +++G++D++VV+T DA++IAHKD QDVKH+VK L G Sbjct: 301 GEVMAYGASNNYVSTEDRLAALVGVQDLLVVDTPDALLIAHKDHAQDVKHIVKRLKNDGH 360 Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVT 411 + H V+RPWG+Y +++ G RF++K I VKP A LSLQMHHHR+EHWIVVSG A V Sbjct: 361 TAHLLHQTVHRPWGTYTTLEDGERFKIKRIVVKPKASLSLQMHHHRSEHWIVVSGMAVVV 420 Query: 412 CDDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 DD+ +L N+ST+I HRL NPG I L +IEVQSG YLGEDDI R ED YGR Sbjct: 421 NDDQELMLNTNESTFIRAGHKHRLQNPGVIDLVLIEVQSGDYLGEDDIVRFEDNYGR 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: 630 Number of extensions: 31 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: 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