Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate BWI76_RS07920 BWI76_RS07920 methionine aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Koxy:BWI76_RS07920 Length = 386 Score = 169 bits (429), Expect = 9e-47 Identities = 113/376 (30%), Positives = 186/376 (49%), Gaps = 17/376 (4%) Query: 16 TVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELRE 75 T+ AL + Q ++L + G PDFD P +++E +AQG +YAP G+ LRE Sbjct: 18 TIFSQMSALAQQHQAINL---SQGFPDFDGPRYLQERLAYHVAQGANQYAPMTGVAALRE 74 Query: 76 ALAEKFRRENGLSVTPEETI-VTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRF 134 A+ +K G + VT G +AL+ A++ GDEVI P + SY + Sbjct: 75 AIVDKTEELYGYRPDANSDVTVTAGATEALYAAITALVRAGDEVICFDPSYDSYAPAIEL 134 Query: 135 AGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAV 194 +GGV+ + P F D ++ +++ +T+ +++N+P+NP+ V+ +E AL + Sbjct: 135 SGGVLKRIALQPPH-FRVDWQQFAASLSDKTRLVILNTPHNPSATVWLREDFAALWQAIA 193 Query: 195 EHDFYLVSDEIYEHLLYEGEHFSPGRVAP---EHTLTVNGAAKAFAMTGWRIGYACGPKE 251 + + Y++SDE+YEH+ + E + P E + V+ K F MTGW++GY P Sbjct: 194 DREIYVLSDEVYEHICFAAEGHASVLAHPQLRERAVAVSSFGKTFHMTGWKVGYCVAPAA 253 Query: 252 VIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALG 311 + + V T + +T AQ A + L + YR RRDL ++ L + Sbjct: 254 ISGELRKVHQYLTFAVNTPAQLAIADMLRREP---EHYRQLPAFYRERRDLFIDALRSSR 310 Query: 312 LKAVRPSGAFYVLMDTSPIAP-DEVRAAERL-LEAGVAVVPGTDFAA--FGH--VRLSYA 365 L+ + G +++L D S ++ D+V L E GVA +P + F A F H +RL +A Sbjct: 311 LEILPCEGTYFLLADYSAVSDLDDVSFCRWLTTEIGVAAIPLSVFCADPFPHKLIRLCFA 370 Query: 366 TSEENLRKALERFARV 381 L A ER R+ Sbjct: 371 KQPATLLAAAERLCRL 386 Lambda K H 0.317 0.133 0.379 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: 339 Number of extensions: 19 Number of successful extensions: 5 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: 385 Length of database: 386 Length adjustment: 30 Effective length of query: 355 Effective length of database: 356 Effective search space: 126380 Effective search space used: 126380 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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