Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 5209529 Shew_1999 aromatic amino acid aminotransferase (RefSeq)
Query= BRENDA::A0A140ND68 (396 letters) >FitnessBrowser__PV4:5209529 Length = 397 Score = 518 bits (1335), Expect = e-152 Identities = 246/396 (62%), Positives = 312/396 (78%) Query: 1 MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENE 60 +F + APADPILGL D F+AD R K+NLG+G+YKDE+G+TP+L SVK AEQ LLE E Sbjct: 2 IFNQVVLAPADPILGLTDAFKADPRADKVNLGVGIYKDESGQTPILKSVKLAEQKLLETE 61 Query: 61 TTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV 120 T+K+YLGIDG+ + + Q LLFG A++++KRA TAQ PGGTG+LR+AA+F+ +NT+ Sbjct: 62 TSKSYLGIDGVIAYNQAVQGLLFGTDHAVMSEKRAVTAQAPGGTGSLRMAAEFVVRNTAS 121 Query: 121 KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGC 180 + VWVSN +W NH ++F SAGL V++Y YYDA +H +DFDA++ SL +A +GD++L HGC Sbjct: 122 RTVWVSNLTWANHNNIFQSAGLTVKQYGYYDAASHDIDFDAMLTSLEQANSGDLLLLHGC 181 Query: 181 CHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV 240 CHNPTGID + QW+ +AQL V+KG +PLFDFAYQGF G+EEDA+GLR A+ EL+V Sbjct: 182 CHNPTGIDLNICQWEVIAQLCVDKGLIPLFDFAYQGFGAGVEEDAQGLRLVASKVPELLV 241 Query: 241 ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSN 300 A+S+SKNFGLYNER+GA TLVA D ET RAFSQ+K+ IR++YSNPPAHGA +VATIL + Sbjct: 242 ANSFSKNFGLYNERIGAVTLVAEDEETAKRAFSQIKSTIRSSYSNPPAHGALIVATILGD 301 Query: 301 DALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR 360 LR +WE+ELT MR+RI MR LFV TL E+G +DFSFI QNGMFSFSGL K+QV R Sbjct: 302 AELRKLWEEELTQMRERIAEMRVLFVKTLSEQGVEQDFSFISAQNGMFSFSGLNKDQVAR 361 Query: 361 LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396 L+EEFGVY V SGR++VAGMT NM +C AI VL Sbjct: 362 LKEEFGVYIVGSGRISVAGMTRANMDTICRAIAQVL 397 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: 480 Number of extensions: 10 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: 397 Length adjustment: 31 Effective length of query: 365 Effective length of database: 366 Effective search space: 133590 Effective search space used: 133590 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