Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 7024674 Shewana3_1852 histidinol phosphate aminotransferase (RefSeq)
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__ANA3:7024674 Length = 401 Score = 133 bits (335), Expect = 7e-36 Identities = 103/333 (30%), Positives = 165/333 (49%), Gaps = 24/333 (7%) Query: 41 SNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILE 100 +NE+P A+ + S+L RYP+ L A S+ GV + G+++ +E Sbjct: 80 ANESPFNNVAVAELDL----SKLNRYPECQPPALINAYSQYSGVVESKIVASRGADEAIE 135 Query: 101 IAAHAFVEKG-QSIVYAQYSFAVYALATQ--GLGARAIVVPAVKYGHDLDAMLAAVSDDT 157 + AF G SI ++ +YA++ Q +G +A+ + A +YG L A A + Sbjct: 136 LLIRAFCVPGIDSIATFGPTYGMYAISAQTFNVGVKALSLTA-EYG--LPADFATAARGA 192 Query: 158 RLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYP 217 +L+F+ NPNNPTGT I+ ++E + +P +VVV DEAY E+ P+ Y + YP Sbjct: 193 KLVFICNPNNPTGTVIDKARIEQAIQALPDAIVVV-DEAYIEFCPE---YSVADLLESYP 248 Query: 218 NLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLE 277 NL+V RT SKAF LAG R GF +A E+ +++ RV P+ V A+ AL+ Sbjct: 249 NLVVLRTLSKAFALAGARCGFLLANEEIIEIIMRVIAPYPVPLPVSEVAVQALSAAGIAR 308 Query: 278 KSA---ALNAQGYR---RLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQG 331 LNAQG R L ++ G + +GN+VL DD A +V L+ G Sbjct: 309 MKTQVKELNAQGERLAAALNLYCEQWGGAVLTPNGNYVLAEF--DDVA--KVAQLLIDNG 364 Query: 332 VIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364 ++ R + L + +R + + + ++ E Sbjct: 365 IVARAYKDPRLAKAIRFSFSSQADTDRLVSLFE 397 Lambda K H 0.318 0.135 0.385 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: 364 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 370 Length of database: 401 Length adjustment: 30 Effective length of query: 340 Effective length of database: 371 Effective search space: 126140 Effective search space used: 126140 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 (21.7 bits) S2: 50 (23.9 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