Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012971277.1 ALVIN_RS10385 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000025485.1:WP_012971277.1 Length = 370 Score = 384 bits (986), Expect = e-111 Identities = 193/366 (52%), Positives = 259/366 (70%), Gaps = 5/366 (1%) Query: 4 SFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASEL 63 S ++ + PY+ GKP+SE+ RE G+ ++ VKLASNENPLG A+ AMA +EL Sbjct: 10 SLAAPWIAGLTPYVPGKPVSELERELGISDS--VKLASNENPLGPGPRAREAMAAVLAEL 67 Query: 64 GRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVY 123 GRYPD FEL+ AL+E +G+ VT+GNGSND+L++ A F+ G V+++++FAVY Sbjct: 68 GRYPDGGGFELRRALAEYHGLSPTAVTIGNGSNDVLDLIARVFLHPGAESVFSEHAFAVY 127 Query: 124 ALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLD 183 +A Q +GA A V A YGHDLDAM V+D TR++++ANPNNPTGT++ L++F+ Sbjct: 128 PIAIQSVGATARVAKARDYGHDLDAMARLVNDRTRVVWIANPNNPTGTWLAAEPLKSFIG 187 Query: 184 KVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQP 243 +P+ +VV+DEAYTEY+ + D+ WV +PNL+V+RTFSKA GLA LRVG+A++ P Sbjct: 188 SLPKTCIVVVDEAYTEYVAEPDFPDATHWVETFPNLIVTRTFSKAHGLAALRVGYALSDP 247 Query: 244 ELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVP 303 + DLLNRVRQPFNVN LAQAAAIAA+ND+ + S LN G ++LT AF++LGL Y+P Sbjct: 248 RVADLLNRVRQPFNVNALAQAAAIAAINDREHVRASVELNRAGMKQLTGAFERLGLTYIP 307 Query: 304 SDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363 S GNFV V G A +N LL++GVIVRPVGNYG+P LRI++GL EN FIAA Sbjct: 308 SVGNFVTVDCGRPAAP---INEALLRRGVIVRPVGNYGMPNHLRISVGLESENARFIAAF 364 Query: 364 ERTLAA 369 E LA+ Sbjct: 365 EDVLAS 370 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: 442 Number of extensions: 14 Number of successful extensions: 3 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: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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: 49 (23.5 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