Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_083818560.1 PYRFU_RS07100 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000223395.1:WP_083818560.1 Length = 386 Score = 155 bits (391), Expect = 2e-42 Identities = 118/343 (34%), Positives = 180/343 (52%), Gaps = 25/343 (7%) Query: 36 IVKLASNENPLGMPESAQRAMAQAASELGRYPDANAF-ELKAALSERYGVPADWVTLGNG 94 I L NE P P Q A+ +AA RYP + + ++ +++ G+ D+V L G Sbjct: 57 ITYLDLNECPFEPPAFVQEAVCKAARRGNRYPTLDDYYTVERLIADYAGLEPDYVVLTAG 116 Query: 95 SNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHD-----LDAM 149 ++ L FV G +V + FA+ T G V AVK + LD Sbjct: 117 GDEALRAIFDVFVGPGDRVVLLEPGFAMTRFYTIVRGG---VYQAVKLREEGRRFLLDEN 173 Query: 150 -LAAVSDDTRLIFVANPNNPTGTFIEGPKLEA-FLDKVPRHVVVVLDEAYTEYLPQEKRY 207 L V+ R+I + NP+NPTG+ + +L LD+ +VV DEAY E+ Sbjct: 174 ELLEVASGARMIVIENPHNPTGSLLANEELAIRLLDETD--AIVVFDEAYYEFAGL---- 227 Query: 208 DSIAWV-RRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAA 266 SIA + +RY L+V RT SKAF LAG RVG+ +A P ++LL + PFN++ + AAA Sbjct: 228 -SIARLTQRYDRLIVVRTLSKAFCLAGYRVGYILAHPTASELLRKALTPFNLSVVQLAAA 286 Query: 267 IAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLE 326 AAL ++ ++EK A R+T+ ++LGL S NF+LV+ G D ++ Sbjct: 287 QAALENRDYVEKVIAHVNSEKDRMTKRLEELGLRVYESYTNFLLVKTGVPD-----IHEL 341 Query: 327 LLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLAA 369 L K GV+V+ + + G ++R+TIG EEN+ FI A+E+ +A+ Sbjct: 342 LAKHGVVVKQIKSLG-SDYIRVTIGTREENDKFIHAIEQAVAS 383 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: 350 Number of extensions: 17 Number of successful extensions: 4 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: 370 Length of database: 386 Length adjustment: 30 Effective length of query: 340 Effective length of database: 356 Effective search space: 121040 Effective search space used: 121040 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 10 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