Align Kynurenine--oxoglutarate transaminase 1; Kynurenine--oxoglutarate transaminase I; Cysteine-S-conjugate beta-lyase; Glutamine transaminase K; GTK; Glutamine--phenylpyruvate transaminase; Kynurenine aminotransferase 1; Kynurenine aminotransferase I; KATI; EC 2.6.1.7; EC 4.4.1.13; EC 2.6.1.64 (characterized)
to candidate PfGW456L13_4856 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::Q08415 (423 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4856 Length = 382 Score = 222 bits (566), Expect = 1e-62 Identities = 139/408 (34%), Positives = 203/408 (49%), Gaps = 34/408 (8%) Query: 9 RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAF-QQATSGNFMLNQYTRAF 67 +L + ++ + +L + +NL QGFPDF+ P A + SG+ NQY+ Sbjct: 5 KLPNVGITIFTQMSQLAAQTGALNLSQGFPDFAAPQALCDAVGRHIASGH---NQYSPMT 61 Query: 68 GYPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDC 127 G P L +A+ + G ++D T V VT GA A+F QA++ GDEVI+ +PA+D Sbjct: 62 GLPVLRQQIAAKIARSYGVQVDVDTEVTVTPGATEAIFCAIQAVIHSGDEVIVFDPAYDS 121 Query: 128 YEPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPL 187 YEP +AGG V V L ND+ +D +LA +PRT++++LNTP+NP Sbjct: 122 YEPSVELAGGRCVHVQL-----------GLNDFSIDFEKLAQALSPRTRMIILNTPHNPS 170 Query: 188 GKVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGK 247 G + SR EL+ +A L + D+ ISDEVY+ LVYDG HVS+ + ++ R + S GK Sbjct: 171 GALISRDELDQLATLIRDRDIYVISDEVYEHLVYDGVPHVSVLAHEELYQRAFVVSSFGK 230 Query: 248 SFSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFL 307 ++ TGWK G+V+ P + LR VHQ F T Q A+A +H Sbjct: 231 TYHVTGWKTGYVIAPPALTAELRKVHQYVNFCGVTPLQYALADFMAEHPEHVE------- 283 Query: 308 QLPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFA 367 +LP + RD L G+YF + D S + PDL E A Sbjct: 284 ELPAFYQAKRDLFCDLLVPSRFSFTRVTGTYFQLVDYSQIR---PDLNDVE-------MA 333 Query: 368 KWMIKNMGLVGIPVSTFFSRPHQKDFDHYIRFCFVKDKATLQAMDERL 415 WM + G+ IP+S F+ P +R CF K + TL+ E+L Sbjct: 334 LWMTREHGVASIPISVFYQTPPVG--QRLVRLCFAKREETLREAAEKL 379 Lambda K H 0.322 0.137 0.431 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: 449 Number of extensions: 15 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: 423 Length of database: 382 Length adjustment: 31 Effective length of query: 392 Effective length of database: 351 Effective search space: 137592 Effective search space used: 137592 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 (21.9 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