Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate CA265_RS03630 CA265_RS03630 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >FitnessBrowser__Pedo557:CA265_RS03630 Length = 346 Score = 180 bits (457), Expect = 4e-50 Identities = 115/358 (32%), Positives = 191/358 (53%), Gaps = 25/358 (6%) Query: 3 IKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62 ++E++K L+PY + E+ V L +NEN YG A YP Sbjct: 7 VRENIKNLRPYS------TARDEFKGQASVFLDANENSYGSPLPAN---------YNRYP 51 Query: 63 DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLND-KTNTVTAAPTFPQYKHN 121 D L+ +SK V + GNGSDE I ++ RAF N K N + PT+ Y+ + Sbjct: 52 DPLQLDLKDAISKIKGVPIENTFLGNGSDEAIDLLFRAFCNPGKDNVIVLPPTYGMYEVS 111 Query: 122 AVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 A I E+R+++L P+ D++ + E ID+ T++++ICSPNNPTG + ++ L Sbjct: 112 ANINDVEIRKVSLLPNFQLDMEKIAETIDKNTKLIFICSPNNPTGNSINREDIETILANF 171 Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENL 241 +VV+DEAY Y + + + L++Y NL++L+TFSKA+GLAALR+G + + Sbjct: 172 NG--IVVVDEAYINYARQKTF---IQELTEYGNLVVLQTFSKAWGLAALRLGMAFSSTKV 226 Query: 242 IRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGL--KCYP 299 I + + P+N ++ Q A AL + A + ++++ A + + K YP Sbjct: 227 IDVLNKIKPPYNINQATQDLAFEALKNIAQVNDWIKESVAERDRLSKALTALNIVKKVYP 286 Query: 300 SQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGF-PTSLRITIGTKEQNEEILAIL 356 S NF+L + A +++ L+++G IVR + + LRIT+GTKE+N+++L +L Sbjct: 287 SDANFILTEV-TDALKIYDTLVDQGIIVRDRSKVTLCEGCLRITVGTKEENDKLLTVL 343 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: 296 Number of extensions: 20 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: 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