Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 5209481 Shew_1951 aromatic amino acid aminotransferase (RefSeq)
Query= BRENDA::A0A140ND68 (396 letters) >FitnessBrowser__PV4:5209481 Length = 396 Score = 404 bits (1038), Expect = e-117 Identities = 198/396 (50%), Positives = 266/396 (67%) Query: 1 MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENE 60 MFEN++ PADPILGL FR D K++LG+GVYKDE G TP+L VK+AEQ+ ++ E Sbjct: 1 MFENLSPMPADPILGLMTKFREDPHANKVDLGVGVYKDEAGNTPILACVKRAEQHRIDTE 60 Query: 61 TTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV 120 TK Y+G G P F + EL FG+ + + R RT TPGGTGALRVAADF+ + Sbjct: 61 ATKVYIGPTGSPAFNQLMGELAFGQDNPALLADRIRTVSTPGGTGALRVAADFIKRVNPN 120 Query: 121 KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGC 180 +WVS+P+W NH +F +AG++V+ Y YYD +N TL FD ++ +L++ A DVVLFH C Sbjct: 121 SVIWVSDPTWANHTGLFEAAGIKVKTYPYYDYQNKTLKFDEMLAALSQIGADDVVLFHAC 180 Query: 181 CHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV 240 CHNP+G+D T EQW + L+ ++G+ PL D AYQGF G++EDA G+R AA ++I+ Sbjct: 181 CHNPSGMDLTNEQWDQVIALTKQQGFTPLIDMAYQGFGDGVDEDAYGVRQMAANVDDMIL 240 Query: 241 ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSN 300 SS SKNFGLY ER+GAC++V DS + + A+S + +R YS PPAHGA++V TIL + Sbjct: 241 CSSCSKNFGLYRERIGACSIVGKDSHSANVAYSVLLYVVRCIYSMPPAHGAAIVETILGS 300 Query: 301 DALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR 360 L+ W EL MR RI R + VN L EKG RDFSFI KQ GMFSF G+T EQV + Sbjct: 301 SELKQQWLDELKVMRDRINGNRAMLVNKLIEKGVTRDFSFIAKQKGMFSFLGVTPEQVAK 360 Query: 361 LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396 L+ + +Y V S R+++AG+ N+ L E+I VL Sbjct: 361 LQADHSIYMVDSSRISIAGIGEGNVDYLAESIAKVL 396 Lambda K H 0.318 0.134 0.392 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: 417 Number of extensions: 12 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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 Aug 03 2021. The underlying query database was built on Aug 03 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