Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_017597555.1 D471_RS0104655 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::O69689 (435 letters) >NCBI__GCF_000341125.1:WP_017597555.1 Length = 423 Score = 446 bits (1146), Expect = e-130 Identities = 219/402 (54%), Positives = 277/402 (68%), Gaps = 1/402 (0%) Query: 19 QQDYAALQGMKLALDLTRGKPSAEQLDLSNQLLSLPGDDYRDPEGTDTRNYGGQHGLPGL 78 ++DY L G L LDLTRGKP+ EQLDLS LLSLPGD + +GTD RNYGG GLP L Sbjct: 18 RRDYKELAGRGLKLDLTRGKPAPEQLDLSEDLLSLPGDLHTAADGTDVRNYGGLRGLPEL 77 Query: 79 RAIFAELLGIAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRPWIQEQDGIKFLCPVPG 138 R IFA++L + L+A NSSLELMHD + ++L + W +Q+ I FLCPVPG Sbjct: 78 REIFADVLQVPAGQLLAAGNSSLELMHDCLVHALLSVLPGADARWA-DQERIVFLCPVPG 136 Query: 139 YDRHFAITETMGIEMIPIPMLQDGPDVDLIEELVAVDPAIKGMWTVPVFGNPSGVTYSWE 198 YDRHFA+ E GIEM+ +PM + GPD+D++E LVA DPA+KG+W VP + NP GV Y E Sbjct: 137 YDRHFALCERFGIEMVAVPMNESGPDMDVVERLVAEDPAVKGIWCVPKYSNPDGVVYGDE 196 Query: 199 TVRRLVQMRTAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAKAGNPNRPYVFASTSKI 258 TV RL +M TAAPDFR+FWDNAYA H LT + D+L A++GNP+R +VF STSKI Sbjct: 197 TVARLARMETAAPDFRIFWDNAYAAHHLTEESVEIADLLAACAESGNPDRAFVFGSTSKI 256 Query: 259 TFAGGGVSFFGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFGDADGVRLHMLRHQQIL 318 TFAG GV FFG S N+ W K+SIGPDKVNQLRH+RF DADG+R HM R + +L Sbjct: 257 TFAGAGVGFFGSSTANVDWLTANNSKRSIGPDKVNQLRHVRFLRDADGLRAHMERQRDLL 316 Query: 319 APKFALVAEVLDQRLSESKIASWTEPKGGYFISLDVLPGTARRTVALAKDVGIAVTEAGA 378 PKFA V +L++ L + +A+WT+P+GGYF++L+V G A+ V A + GI +T AGA Sbjct: 317 KPKFAAVQRILEEELGGTGLATWTDPRGGYFVTLEVPEGCAKEVVRRASEAGIVLTPAGA 376 Query: 379 SFPYRKDPDDKNIRIAPSFPSVPDLRNAVDGLATCALLAATE 420 + PY DP D IRIAPSFP++ +L A+ GL C L E Sbjct: 377 THPYGDDPRDATIRIAPSFPTLAELEQAMLGLTVCVRLVGYE 418 Lambda K H 0.320 0.138 0.415 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: 603 Number of extensions: 23 Number of successful extensions: 2 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: 435 Length of database: 423 Length adjustment: 32 Effective length of query: 403 Effective length of database: 391 Effective search space: 157573 Effective search space used: 157573 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 (21.8 bits) S2: 51 (24.3 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