Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate Pf6N2E2_5377 Mannose-6-phosphate isomerase (EC 5.3.1.8) / Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)
Query= CharProtDB::CH_121570 (483 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5377 Length = 483 Score = 931 bits (2406), Expect = 0.0 Identities = 453/483 (93%), Positives = 472/483 (97%) Query: 1 MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60 MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR Sbjct: 1 MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60 Query: 61 FIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQKA 120 FIVNEQL+NRKLE QRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVI+DQKA Sbjct: 61 FIVNEQLSNRKLEAQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIEDQKA 120 Query: 121 LQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDEKR 180 LQRALALATVAAERGEMVLFG+P T+PETGYGYIKSTND+LLPEGVSRV FVEKPD KR Sbjct: 121 LQRALALATVAAERGEMVLFGIPPTKPETGYGYIKSTNDALLPEGVSRVSHFVEKPDAKR 180 Query: 181 AVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDATF 240 A EF+++GGYFWNSGMFLFRASRFLEELKKHDPDIYDTC+LTLERSEQTADT+T D+ATF Sbjct: 181 ATEFLEAGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCLLTLERSEQTADTITFDEATF 240 Query: 241 ACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKGDVVIQDSR 300 ACCPDNSIDYAVMEKTQRACVVPL+AGWSDVGCWASLW VN+KD +GNV+KGDVVIQDSR Sbjct: 241 ACCPDNSIDYAVMEKTQRACVVPLAAGWSDVGCWASLWEVNEKDTNGNVTKGDVVIQDSR 300 Query: 301 NCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGRSETQNHCEV 360 NCMIHGNGKLVSVIGL+NIVVVETKDAMMIAHKDKVQGVKQMV+TLN QGR+ETQNHCEV Sbjct: 301 NCMIHGNGKLVSVIGLENIVVVETKDAMMIAHKDKVQGVKQMVNTLNAQGRTETQNHCEV 360 Query: 361 YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLT 420 YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLL Sbjct: 361 YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLC 420 Query: 421 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTPVERGVSVKT 480 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTP+ERGVSVKT Sbjct: 421 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTPIERGVSVKT 480 Query: 481 IAQ 483 IAQ Sbjct: 481 IAQ 483 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: 906 Number of extensions: 25 Number of successful extensions: 1 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: 483 Length adjustment: 34 Effective length of query: 449 Effective length of database: 449 Effective search space: 201601 Effective search space used: 201601 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