Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate Pf1N1B4_1964 Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)
Query= CharProtDB::CH_121570 (483 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1964 Length = 480 Score = 385 bits (988), Expect = e-111 Identities = 208/479 (43%), Positives = 296/479 (61%), Gaps = 11/479 (2%) Query: 1 MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERL--VFEGMDTPIVVCNKD 58 +IPVILSGG+G+RLWP+SR+ PK F+ L +L +T R + +G + V N+D Sbjct: 2 LIPVILSGGAGTRLWPVSREGHPKPFMILPDGQSLLSKTYRRAAGLLDGWGDIVTVTNRD 61 Query: 59 HRFIVNEQLANRKLECQR--ILMEPFGRNTAPAVALTAMML-VNEGRDELMLVLPADHVI 115 + F + LE R L+EP GRNTAPA+A A+ L G + +M+V+PADH+I Sbjct: 62 YYFQSKDHYQEACLERHRGHFLLEPTGRNTAPAIAAAALSLQALHGDEAIMVVMPADHLI 121 Query: 116 DDQKALQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEK 175 ++ AL+ A+ A A+ G +V FGV T PETG+GYI+ T L +G ++VQ+FVEK Sbjct: 122 LNEDALKSAVEHAVALAKSGHLVTFGVVPTAPETGFGYIE-TGAPLDDKGAAKVQRFVEK 180 Query: 176 PDEKRAVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSE--QTADTV 233 PD + A +++SG + WNSGMF F + L EL H P + + + S +T + Sbjct: 181 PDLQTATHYLESGNFLWNSGMFCFSIATLLAELHLHAPALLEQARACMAASAPVETGGCL 240 Query: 234 T--LDDATFACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSK 291 L FA D SIDYA+ME++ + VVP S WSD+G W ++ A+ D N + Sbjct: 241 QQELSPTHFAEITDISIDYALMERSDKVVVVPASFDWSDIGSWGAVAALVPADAQNNRAS 300 Query: 292 GDVVIQDSRNCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGR 351 G+ + DS N + +LV+ +G+DN+++++T DA+++AH D+ Q V+++ L D+ Sbjct: 301 GEAIFIDSHNNFVQSEDRLVAAVGVDNLIIIDTADAVLVAHADRAQDVRRVARQLKDKKH 360 Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVT 411 + H V RPWG+Y ++ G RF++K I VKPGA LSLQMHHHR EHW+VV G A+VT Sbjct: 361 EAYRLHRTVSRPWGTYTVLEEGPRFKIKRIVVKPGAKLSLQMHHHRNEHWVVVEGMAKVT 420 Query: 412 CD-ENVFLLTENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRS 469 + L+ +N+ST+I HRL NPG I L IIEVQSG YLGEDDI RFED YGR+ Sbjct: 421 NNGSGSHLVAKNESTFIAAGHRHRLENPGVIDLVIIEVQSGEYLGEDDIVRFEDQYGRT 479 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: 623 Number of extensions: 24 Number of successful extensions: 6 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: 480 Length adjustment: 34 Effective length of query: 449 Effective length of database: 446 Effective search space: 200254 Effective search space used: 200254 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