Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_092482850.1 BM299_RS07475 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_900115975.1:WP_092482850.1 Length = 370 Score = 264 bits (675), Expect = 3e-75 Identities = 153/362 (42%), Positives = 215/362 (59%), Gaps = 9/362 (2%) Query: 10 VRAIAPY---IAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRY 66 VR + P+ + P E+ + GL + KL+ NEN G A AM +AA E+ Y Sbjct: 11 VRELKPFPRELPDLPGEEIKKRLGLTH--VDKLSFNENLNGPSPLAVEAMQKAAQEVHLY 68 Query: 67 PDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALA 126 P + L AL+E YGV + L NG+++++ +AA F G ++V++ SF YA+A Sbjct: 69 PSSYGDALCRALAEFYGVETGNLLLSNGADEMIYLAAQTFAGPGDAVVFSTPSFGAYAVA 128 Query: 127 TQGLGARAIVVPAVKYGHDLDAMLAAVSDD-TRLIFVANPNNPTGTFIEGPKLEAFLDKV 185 + LGA + VP Y DL AMLA D LIF+ NPNNPTGT + + F+ V Sbjct: 129 ARLLGADPLPVPLTGYAVDLTAMLARAQDPGVGLIFICNPNNPTGTMVAPEDIRDFMQNV 188 Query: 186 PRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPEL 245 P ++VV++DEAY EY +++ + R+PNL V RTFSK +GLAG RVG+ +A E+ Sbjct: 189 PSNIVVMVDEAYMEYTRDPAGLSAVSLINRFPNLGVIRTFSKIYGLAGARVGYLVAGREI 248 Query: 246 TDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSD 305 T +++RVR PFNVN +AQA A+AAL D+ +E+ LN R L AF++LGL+YVPS Sbjct: 249 TQMMHRVRLPFNVNGIAQAGALAALRDRGHVERVRQLNDGQRRYLESAFERLGLKYVPSC 308 Query: 306 GNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALER 365 NF+LV G D V EL ++GVIVRP +GL +LR++IG E N FI +L+ Sbjct: 309 TNFILVDTGRD---SRTVFAELAQRGVIVRPGFQFGLDTFLRVSIGTEEANRRFIVSLQE 365 Query: 366 TL 367 L Sbjct: 366 IL 367 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: 346 Number of extensions: 16 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