Align aromatic-amino-acid transaminase [EC:2.6.1.57] (characterized)
to candidate WP_090219958.1 CV091_RS15685 aspartate/tyrosine/aromatic aminotransferase
Query= reanno::Phaeo:GFF2895 (394 letters) >NCBI__GCF_002796795.1:WP_090219958.1 Length = 394 Score = 666 bits (1719), Expect = 0.0 Identities = 325/394 (82%), Positives = 360/394 (91%) Query: 1 MFETLKPQPADKILALMQMYRDDPRDSKIDLGVGVYKNAEGVTPVMRAIKAAEHKLWEEQ 60 MFE LK PADKILALMQM+R+DPR++K+DLGVGVYKNAEGVTPVMRA+KAAE ++WEEQ Sbjct: 1 MFENLKAPPADKILALMQMFREDPRENKVDLGVGVYKNAEGVTPVMRAVKAAEQQIWEEQ 60 Query: 61 TSKSYVGLAGDPAYSDAMIKLILSDSVARANVAAAATPGGTGAVRQAFELIKMANPGARV 120 SKSYVGLAGDPAYS AMI+LIL D+VAR N+AA ATPGGTGAVRQAFEL++ NP ARV Sbjct: 61 GSKSYVGLAGDPAYSAAMIQLILGDTVARENIAAVATPGGTGAVRQAFELVRNTNPDARV 120 Query: 121 FVSNPTWPNHISILNYLNIETVAYRYFDRETCGVDFDGMIADLKTANKGDVVLLHGCCHN 180 FVS+PTWPNH+SIL YLN+ETV YRYFDRET GV+FDGMI DLK A GDVVLLHGCCHN Sbjct: 121 FVSDPTWPNHVSILKYLNMETVTYRYFDRETRGVNFDGMIEDLKAAKTGDVVLLHGCCHN 180 Query: 181 PTGANLNMVQWQEVVAILNERGLIPMIDIAYQGFGDGLEEDAQGVRYVAANTPECLIAAS 240 PTGANLN VQW+EV+A++N +GLIPM+DIAYQGFGDGLEEDA GVR VA++ PE LIAAS Sbjct: 181 PTGANLNEVQWREVIALINAQGLIPMVDIAYQGFGDGLEEDAMGVRLVASSCPEVLIAAS 240 Query: 241 CSKNFGIYRERTGLLMAVSQDSGAQALNQGTLAFLNRQNYSFPPDHGARLVSMILNDDAL 300 CSKNFGIYRERTGLL+AVSQD+ AQAL+QG L FLNRQNYSFPPDHGAR+VS I+NDDAL Sbjct: 241 CSKNFGIYRERTGLLLAVSQDASAQALHQGNLNFLNRQNYSFPPDHGARIVSTIMNDDAL 300 Query: 301 RADWAAELEETRLGMLALRQQLADELQRLTGSDRFGFLAQHRGMFSLLGTTPEMVEKMRA 360 R DWAAELEETRLGML LRQQLADELQRLTGSDRF FLAQHRGMFSLLGTTP++VEKMR Sbjct: 301 RGDWAAELEETRLGMLGLRQQLADELQRLTGSDRFAFLAQHRGMFSLLGTTPDLVEKMRV 360 Query: 361 ESGIYMVGDSRMNIAGLNTQTVPILAQAIVDAGV 394 ++GIYMVGDSRMNIAGLN Q+VPILAQAIVDAGV Sbjct: 361 DNGIYMVGDSRMNIAGLNKQSVPILAQAIVDAGV 394 Lambda K H 0.319 0.135 0.395 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: 566 Number of extensions: 13 Number of successful extensions: 1 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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 (21.8 bits) S2: 50 (23.9 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