Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate BPHYT_RS08530 BPHYT_RS08530 mannose-1-phosphate guanylyltransferase (GDP)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS08530 Length = 405 Score = 175 bits (444), Expect = 2e-48 Identities = 116/304 (38%), Positives = 160/304 (52%), Gaps = 30/304 (9%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIK----RLAFD------------ 46 PVI + G G+R WPLSR++ PK+ + GD +L + T++ RL Sbjct: 28 PVIFADGLGARSWPLSRERNPKRSVDRMGDASLLESTLRTTLSRLDASFVAAHHVTPASS 87 Query: 47 --GMQAPLLVCNKEHRFIVQEQLE--AQNLASQAILLEPFGRNTAPAVAIAAMKLVA--- 99 + APL+VC ++ +E LE A++ S ++L+P R+TAPA+ IAA+ A Sbjct: 88 PRSIAAPLMVCCEDLHRQSREPLERLARSGRSVRMVLQPIARDTAPALTIAALAARAAAV 147 Query: 100 EGRDELLLILPADHVIEDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASAD 159 EG D L++ LPADH I D AF ALA A A G +V G+P R ETG+GYIR A Sbjct: 148 EGDDPLIVALPADHPIADHVAFGVALAEALEHATHGALVALGVPPRRAETGFGYIRTGA- 206 Query: 160 AQLPEGVSRVQSFVEKPDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTC 219 A G ++ FVEKPD A + A G Y+WNSG+F+ RAS +L + I + C Sbjct: 207 ALGKRGARVIERFVEKPDPELAERYAALGNYWWNSGLFVVRASVWLAAIALCHPAIAEAC 266 Query: 220 LLALERSQHDGD-LVNIDAATFECCPDNSIDYAVMEKTS-----RACVVPLSAGWNDVGS 273 A ER+ DGD +++ CP SIDYAVME+ VP AG + Sbjct: 267 AAAFERATVDGDGTLHVARDQLALCPSRSIDYAVMERVGSDARVAGVTVPFVAGRAQACA 326 Query: 274 WSSI 277 W S+ Sbjct: 327 WDSV 330 Score = 69.3 bits (168), Expect = 2e-16 Identities = 36/66 (54%), Positives = 44/66 (66%), Gaps = 1/66 (1%) Query: 409 QVTCDDKTFLLTE-NQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYG 467 +V ++ F+L E N STY P HRLAN G+ P E+IEVQSG +LGEDDI R ED +G Sbjct: 332 RVARGEECFMLAEENPSTYAPPGVTHRLANTGRTPREMIEVQSGGHLGEDDIVRFEDPFG 391 Query: 468 RTAEPA 473 R E A Sbjct: 392 RNLESA 397 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: 464 Number of extensions: 23 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 481 Length of database: 405 Length adjustment: 32 Effective length of query: 449 Effective length of database: 373 Effective search space: 167477 Effective search space used: 167477 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