Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate 349730 BT0202 histidinol-phosphate aminotransferase (NCBI ptt file)
Query= metacyc::BSU22620-MONOMER (360 letters) >FitnessBrowser__Btheta:349730 Length = 346 Score = 171 bits (433), Expect = 3e-47 Identities = 118/347 (34%), Positives = 185/347 (53%), Gaps = 28/347 (8%) Query: 17 KPIEAVKSEY-GLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYPDGYSAALRTRLSK 75 KP + + EY G V L +NENPY L H YPD L+T LSK Sbjct: 16 KPYSSARDEYKGAVASVFLDANENPYN--------LPHN-----RYPDPMQWELKTLLSK 62 Query: 76 HLNVSETSLIFGNGSDEIIQIICRAFLN-DKTNTVTAAPTFPQYKHNAVIEGAEVREIAL 134 VS + GNGSDE I ++ RAF +K N V PT+ Y+ A + E R++ L Sbjct: 63 IKKVSPQHIFLGNGSDEAIDLVFRAFCEPEKDNVVAIDPTYGMYQVCADVNNVEYRKVLL 122 Query: 135 RPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSRVLVVLDEAYY 194 + + +L A DE+T+++++CSPNNPTG E+ L LV+LDEAY Sbjct: 123 DENFQFSAEKLLAATDERTKLIFLCSPNNPTGNDLLRSEIEKILREFEG--LVILDEAYN 180 Query: 195 EYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQIEPAREPFNT 254 ++ A + E L KY NL++ +TFSKA+G AA+R+G A E +I + + P+N Sbjct: 181 DFSEAPSFLEE---LDKYPNLVVFQTFSKAWGCAAIRLGMAFASEAIIGILSKIKYPYNV 237 Query: 255 SRLGQAAAIAAL----DDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNFVLIDFK 310 ++L Q AIA L + + +I + E+ + +++ + T ++ YPS +NF L Sbjct: 238 NQLTQQQAIAMLHKYYEIERWIKTLKEERDYLEEEFAKLSCT--VRMYPSDSNFFLAKV- 294 Query: 311 RPADELFQALLEKGYIVRSGNALGFPTS-LRITIGTKEQNEEILAIL 356 A +++ L+ +G IVR+ +++ + LR+T+GT+ +N +LA L Sbjct: 295 TDAVKIYNYLVGEGIIVRNRHSISLCCNCLRVTVGTRVENNTLLAAL 341 Lambda K H 0.317 0.134 0.382 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: 344 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: 360 Length of database: 346 Length adjustment: 29 Effective length of query: 331 Effective length of database: 317 Effective search space: 104927 Effective search space used: 104927 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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