Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Smeli:SMc01578 Length = 400 Score = 223 bits (569), Expect = 6e-63 Identities = 131/372 (35%), Positives = 202/372 (54%), Gaps = 16/372 (4%) Query: 30 QGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQA 89 +G +++ L G+PDFDTP I +AAID++ G T Y V G LR+ IA++ +R + Sbjct: 29 KGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIAKKFKRENNLD 88 Query: 90 VDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSEN 149 A Q +V G + L+ LNPGDEV++ P +V+Y + CG V VP R EN Sbjct: 89 YTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGTPVFVPTRQEN 148 Query: 150 GFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYS 208 F+++AE++ ITP+T+ NSP NPSGA+ +AL ++ M H +W+++D++Y Sbjct: 149 NFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPHVWVLTDDMYE 208 Query: 209 ELLF-DGEHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCM 266 L + D +P + PG+ +RT T+N +SK++AMTGWR+G+ GP L ++ + Sbjct: 209 HLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLIKAMDMIQGQQ 268 Query: 267 LYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFV-- 324 G+ Q AA AL P + +E ++ RRDLV+ L + G+ P+G +V Sbjct: 269 TSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCPTPEGAFYVYP 328 Query: 325 -----MVDIRPTGL---SAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLR 376 + P+G + + F LL+ GV+V+ G AFG + R+ L Sbjct: 329 SCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG--LGPNFRISYATSEALLE 386 Query: 377 EACRRI-ALCAA 387 EACRRI CAA Sbjct: 387 EACRRIQRFCAA 398 Lambda K H 0.322 0.136 0.411 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: 397 Number of extensions: 22 Number of successful extensions: 3 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: 393 Length of database: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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 Sep 17 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