Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_066326077.1 BLR17_RS14015 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_900100165.1:WP_066326077.1 Length = 349 Score = 173 bits (439), Expect = 5e-48 Identities = 116/365 (31%), Positives = 190/365 (52%), Gaps = 34/365 (9%) Query: 3 IKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62 I+E++K LKPY + ++ ++V L +NENPY + YP Sbjct: 10 IRENVKVLKPYSSARD---EFEDFDTAEMVFLDANENPYQ-------------NGVNRYP 53 Query: 63 DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKT-NTVTAAPTFPQYKHN 121 D A ++ L N++ ++ GNGSDE++ ++ RAF K N +T PT+ Y Sbjct: 54 DPQQANVKVALGAIKNLNPQQILLGNGSDEVLDLLFRAFCEPKVDNVITLPPTYGMYGVL 113 Query: 122 AVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 A I E +EI L D +D +LEA+ T+++++CSPNNPTG + + LE+ Sbjct: 114 ANINNVENKEILLTNDFQPQVDKILEAVTPTTKLIFLCSPNNPTGNSFTTESVTTLLEKF 173 Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENL 241 VV+DEAY ++ D + L +Y NL+I +T SKAYGLA +R+G A + Sbjct: 174 NG--FVVIDEAYIDF---SDKASWLEKLDQYPNLIITQTLSKAYGLAGIRLGICYASTEV 228 Query: 242 IRQIEPAREPFNTSRLGQAAAIAALDDQ----AFIASCVEQNNAGLQ--QYYDFAKTHGL 295 I + + P+N + L Q A+ L+DQ I+S +E+ + L + F + Sbjct: 229 IAVLNKIKPPYNVNELTQQRALERLNDQEKINREISSILEERDTLLDVLNHVSFVE---- 284 Query: 296 KCYPSQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGF-PTSLRITIGTKEQNEEILA 354 K YP++ NF+LI A++ + L+ KG ++R+ +LR+TIGT E+N++++ Sbjct: 285 KIYPTEANFILIKVD-DANKRYDELIAKGIVIRNRTTQPLCENTLRLTIGTAEENKKLMK 343 Query: 355 ILAEI 359 L E+ Sbjct: 344 ALTEL 348 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: 332 Number of extensions: 23 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: 349 Length adjustment: 29 Effective length of query: 331 Effective length of database: 320 Effective search space: 105920 Effective search space used: 105920 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 Jul 26 2024. The underlying query database was built on Jul 25 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