Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate GFF3926 PGA1_65p00290 algA: alginate biosynthesis protein
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Phaeo:GFF3926 Length = 473 Score = 431 bits (1108), Expect = e-125 Identities = 219/469 (46%), Positives = 301/469 (64%), Gaps = 3/469 (0%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHRFI 62 P++L GGSG+RLWPLSRK YPKQF+ L G+ TLFQ + RL+ +G AP+++ N + RFI Sbjct: 4 PILLCGGSGTRLWPLSRKSYPKQFVPLVGETTLFQASALRLSGEGFAAPMVLTNSDFRFI 63 Query: 63 VQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAFQ 122 V EQL + AIL+EP GRNTAPAV AA+ L A + L+L+ P+DHV+ D AF+ Sbjct: 64 VTEQLAEAGIDPGAILIEPAGRNTAPAVLAAALWLRARDPEGLMLVAPSDHVVPDAAAFR 123 Query: 123 QALALATNAAEKGEMVLFGIPASRPETGYGYIRASAD-AQLPEGVSRVQSFVEKPDEARA 181 A+A A AA GE+V FGI R ETGYGY+ D V ++ FVEKPD A A Sbjct: 124 AAVAAAEPAARAGELVTFGIKPDRAETGYGYLELDGDPGDFSPKVIGLKRFVEKPDLATA 183 Query: 182 REFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATFE 241 + +A+G + WN+G+FLF + + H D+ A+++ + D + +D A ++ Sbjct: 184 EDMLASGQFLWNAGIFLFSVKAIIAAFETHAPDLMVPVQGAVDQGEPDLGFLRLDPAAWD 243 Query: 242 CCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSHN 301 D SIDYAVME+ VVP + GW+D+G W ++W D +G VT+G + N Sbjct: 244 GAADISIDYAVMERAENLAVVPYAGGWSDLGGWDAVWRESGPDGDGIVTQGRATAIECSN 303 Query: 302 CLVHG--NGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCE 359 L+ +G V IGL+D++ V DA+++A R Q+VK V L A+ + + + Sbjct: 304 SLLRSEDDGLEVVGIGLKDVIAVAMPDAVLVADASRAQEVKKAVAALKAKSARQAEAFPK 363 Query: 360 VYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLL 419 +RPWG ++S+ +G RFQVK I V PGA LSLQ HHHR+EHWIVV GTA+VT DD L+ Sbjct: 364 DHRPWGWFESLVVGERFQVKRIHVHPGAALSLQSHHHRSEHWIVVEGTAKVTVDDSVQLV 423 Query: 420 TENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 +ENQS YIP+ +VHR+ NPGK+P+ +IEVQ+GSYLGEDDI R ED+Y R Sbjct: 424 SENQSVYIPLGAVHRMENPGKVPMVLIEVQTGSYLGEDDIIRYEDIYAR 472 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: 618 Number of extensions: 32 Number of successful extensions: 3 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: 473 Length adjustment: 33 Effective length of query: 448 Effective length of database: 440 Effective search space: 197120 Effective search space used: 197120 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