Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate BPHYT_RS26755 BPHYT_RS26755 aromatic amino acid aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS26755 Length = 399 Score = 559 bits (1441), Expect = e-164 Identities = 272/399 (68%), Positives = 319/399 (79%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 MF+HI AYPGDPILSLNE FQLDPR++KVNLSIGIYFDD G+LPVM AVR AE AL+ + Sbjct: 1 MFDHIPAYPGDPILSLNEDFQLDPRSNKVNLSIGIYFDDAGKLPVMDAVRRAETALLDSI 60 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 GPR YLPMAG YRDA QALVFG +AR GRIAT+QT+GGSGAL+VGADFLKRYFP Sbjct: 61 GPRSYLPMAGLPLYRDAAQALVFGADSEARKAGRIATLQTIGGSGALKVGADFLKRYFPG 120 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180 +Q+WISDPSWENHRV+FE G TVNTYPYYD+ TGGL+F M++ + +P++S+VLLHAC Sbjct: 121 SQIWISDPSWENHRVVFEGAGLTVNTYPYYDEHTGGLRFADMIETIDSLPEQSVVLLHAC 180 Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240 CHNPTGVDL+ QW +L+ +L++ +L+ FVDMAYQGFGAGL++DA VR L G+P + Sbjct: 181 CHNPTGVDLSPAQWAELVPVLQRRKLIAFVDMAYQGFGAGLEEDAACVRLLADAGIPLIA 240 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 ANSFSKNFSLYGER G LSVVC SAEE GRVLGQL VRANYSNPPTHGAR+VA VL Sbjct: 241 ANSFSKNFSLYGERVGALSVVCKSAEEAGRVLGQLMSTVRANYSNPPTHGARLVANVLAD 300 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360 +LR WE ELA ERI MR IH GLA V +RY+ QRGMFTYTGL+ QV+R Sbjct: 301 ASLRASWEAELATMRERILAMRGTIHAGLAGRVDEVMRARYVAQRGMFTYTGLSESQVER 360 Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVLAPA 399 LR+E+ VY+LRSGRMCVAGLNERN VA +IA+V++ A Sbjct: 361 LRSEYAVYVLRSGRMCVAGLNERNAEYVAASIAAVVSGA 399 Lambda K H 0.323 0.137 0.417 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: 534 Number of extensions: 16 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: 400 Length of database: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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