Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 228 bits (581), Expect = 3e-64 Identities = 144/426 (33%), Positives = 228/426 (53%), Gaps = 25/426 (5%) Query: 38 IERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYAQLQTLPF-YNNFFQCTHE 96 + A+GVY+WD G + LD +G N+G+GR I +A AQL + F Y F+ + Sbjct: 17 VSHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFE--NA 74 Query: 97 PAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDLKGMPSKKTIISRKNAYH 156 PA+ LA + + +VFF SGSEA ++ L++ R+Y+ +G P ++ +S + +YH Sbjct: 75 PAVALAKALVGFTQQQLEKVFFVSSGSEAVESALKLARQYFVARGEPQRRRFVSLRPSYH 134 Query: 157 GSTVAGASLGGMGFMHQQG---DLPIPGIVHIDQPYWFGEGRDMSPEAFGI--KTAQALE 211 GST+ +LG G+ + D+ I + ++ + D + T A+E Sbjct: 135 GSTLG--ALGVTGYQPLEAPFRDIAIGSLKVAGPDFYRHDDTDDGRHVARVLADTRAAIE 192 Query: 212 AKILELGEDKVAAFIAEPFQGAG-GVIIPPDSYWNEIKRILEKYNILFILDEVISGFGRT 270 A G D +AAF+ EP GA G SY I+ + +++ L ILDEV++G GRT Sbjct: 193 AA----GPDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRT 248 Query: 271 GNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDGGEFAHGFTYSGHPV 330 G WFA Q G+ PDL++ AKG+ +GY P+G V+ + + +++ GG F HG TY+G+P+ Sbjct: 249 GTWFAYQHYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGG-FQHGHTYAGNPL 307 Query: 331 AAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAH-PLVGEVRGMGMVGAIELVAD 389 A A L + +E E+++D V G L L+ L A P VG+VRG+G++ +ELVAD Sbjct: 308 ACATGLAVVEAIEREKILDNVAA-RGRQLAAGLEALKARFPWVGDVRGLGLLWGVELVAD 366 Query: 390 KHSMVRFGSEISAGMLCREACIESGLVM-------RAVGDTMIISPPLCITRDEIDELIF 442 S F +E + E GL++ GD +I+PPL I + EL+ Sbjct: 367 AASKAPFPAEQNRFARITALAREEGLLIYPRRTLDGIAGDHFLITPPLTIDAADTAELLT 426 Query: 443 KASQAL 448 + +A+ Sbjct: 427 RLERAM 432 Lambda K H 0.321 0.137 0.408 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: 510 Number of extensions: 29 Number of successful extensions: 7 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: 460 Length of database: 450 Length adjustment: 33 Effective length of query: 427 Effective length of database: 417 Effective search space: 178059 Effective search space used: 178059 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 Sep 24 2021. The underlying query database was built on Sep 17 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