Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate GFF3397 PGA1_c34500 3'(2'),5'-bisphosphate nucleotidase CysQ
Query= reanno::Korea:Ga0059261_2035 (260 letters) >FitnessBrowser__Phaeo:GFF3397 Length = 265 Score = 73.2 bits (178), Expect = 5e-18 Identities = 74/246 (30%), Positives = 111/246 (45%), Gaps = 21/246 (8%) Query: 8 IDLAGRLADAAGAAIRPYFRA-EHGLESKDDSSPVTLADKAAEAAMRRLIIAERPMDAII 66 I + RLA AG I + + E ++ K D SPVT AD+AA+A + + A P ++ Sbjct: 7 IPVIRRLAIEAGEKIMEIYNSDEFEVKVKSDESPVTAADEAADALISAGLRAAFPDVMLV 66 Query: 67 GEEEDDRPGTSGRIW-VLDPIDGTRSFIVGRPIFGTLIALLEDGWPVLGIIDQPIIKERW 125 EE+ D SG + ++DP+DGT+ FI R F IAL+E G P G++ P + Sbjct: 67 TEEQADSHSKSGDTFLIVDPLDGTKEFIHRRGDFTVNIALVEKGVPTRGVVYAPARSRMF 126 Query: 126 L----GVTGRET-----LFNGKPARARTCRELSKALLATTSPA---LFTDGQLHAFEHVD 173 G ET G+ R + AL+ S + TD ++ + Sbjct: 127 FTLADGSAVEETGAFDPAAMGEIKPIRVADSNNDALMVVASKSHRDQATDDYINKY---- 182 Query: 174 AAVMSTVLGGDCYNYGLVASGHLDIVIEAGLKLH-DFAALVPVVEGAGGRMCDWQGD-PL 231 AV + G + LVA+G D+ G + D AA V+ GAGG++ + PL Sbjct: 183 -AVKDSKSAGSSLKFCLVATGEADLYPRVGRTMEWDTAAGHAVLGGAGGQVVRFDDHAPL 241 Query: 232 HAGSNG 237 G G Sbjct: 242 TYGKEG 247 Lambda K H 0.320 0.138 0.419 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: 161 Number of extensions: 8 Number of successful extensions: 2 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: 260 Length of database: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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