Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_011882167.1 aromatic amino acid aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >NCBI__GCF_000016205.1:WP_011882167.1 Length = 400 Score = 615 bits (1587), Expect = 0.0 Identities = 305/396 (77%), Positives = 332/396 (83%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 MFEHIDAYPGDPIL+LNE+FQ DPR KVNLSIGIYFD +GR+PVM AVREAE AL D+ Sbjct: 1 MFEHIDAYPGDPILTLNENFQKDPRDQKVNLSIGIYFDADGRIPVMAAVREAETALQRDV 60 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120 GP+PYLPM G AAYRDAVQALVFG ARA GRIATVQTLGGSGAL+VGADFLKRYFPD Sbjct: 61 GPKPYLPMVGLAAYRDAVQALVFGADHPARAAGRIATVQTLGGSGALKVGADFLKRYFPD 120 Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180 AQVW+SDPSWENHR IFER GFTVNTYPYYD ATGGLKFDAML A+ +P RSIVLLHAC Sbjct: 121 AQVWLSDPSWENHRFIFERAGFTVNTYPYYDAATGGLKFDAMLAAIDALPARSIVLLHAC 180 Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240 CHNPTGVDL+ QW +LI +++ ELLPFVDMAYQGFGAGLD DAFAVREL +GVP LV Sbjct: 181 CHNPTGVDLDEGQWEKLIDVIEARELLPFVDMAYQGFGAGLDADAFAVRELARRGVPALV 240 Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300 ANSFSKNFSLYGER G LSVVC+ A+ RVLGQL GAVR+NYSNP T+GA++VA VL T Sbjct: 241 ANSFSKNFSLYGERVGALSVVCEDADAAERVLGQLAGAVRSNYSNPQTYGAKLVATVLNT 300 Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360 PALR WE ELA C RIA+MR AIH GL HVSGEAL+RY+ QRGMFTYTGLT QVD Sbjct: 301 PALRKQWEEELAAMCRRIARMRQAIHDGLRDHVSGEALTRYVKQRGMFTYTGLTETQVDA 360 Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 LR HGVY+LRSGRMCVAGLN+ NV VA AI VL Sbjct: 361 LRDVHGVYILRSGRMCVAGLNDSNVGIVADAIGKVL 396 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: 573 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: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 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