Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate Echvi_3798 Echvi_3798 Mannose-1-phosphate guanylyltransferase
Query= CharProtDB::CH_121570 (483 letters) >FitnessBrowser__Cola:Echvi_3798 Length = 333 Score = 202 bits (514), Expect = 1e-56 Identities = 126/349 (36%), Positives = 191/349 (54%), Gaps = 25/349 (7%) Query: 1 MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60 ++ V+LSGG GSRLWPLSRK PKQ+L + TLFQ+T+ R D +VV NKD+ Sbjct: 4 IVNVVLSGGVGSRLWPLSRKSRPKQYLPIFDGETLFQKTVARNRSIA-DEVLVVGNKDNY 62 Query: 61 FIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQKA 120 + + +A KL R L+E RNTA A+A +A E +++ V P+DH+I A Sbjct: 63 ELSRKDMAASKLSQYRELVEACPRNTAAAIAFSAFHCHEE---DVLFVTPSDHLITPGTA 119 Query: 121 LQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDEKR 180 Q A+ A A G +V FG+ + PETGYGYI++ + V+ F EKP++++ Sbjct: 120 YQTAVKRAIQLANEGNIVTFGLKPSHPETGYGYIEAVGED--------VKDFHEKPEQEK 171 Query: 181 AVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDATF 240 A F K GGY WNSGMF F+A FL EL++++ +I+D ++ + L + Sbjct: 172 ADNFFKQGGYLWNSGMFCFQAGVFLAELRRYETEIFDQAYGAYMLKKE----IFLPETES 227 Query: 241 ACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKGDVVIQDSR 300 P S+DYAVME++++ VV WSD+G + +++ K H + DS Sbjct: 228 LRIPSLSVDYAVMERSKKIKVVAADFEWSDMGSFEAIYDYLGKKGHH--------LDDSG 279 Query: 301 NCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQ 349 N M+ G + GL N +++ TKDA++ K+ Q VK + L ++ Sbjct: 280 N-MVIGTNTHIEFTGLTNTLLIFTKDAVLALKKENSQEVKDVFQRLENE 327 Lambda K H 0.319 0.135 0.405 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: 382 Number of extensions: 22 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: 483 Length of database: 333 Length adjustment: 31 Effective length of query: 452 Effective length of database: 302 Effective search space: 136504 Effective search space used: 136504 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: 50 (23.9 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