Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_011382998.1 AMB_RS02875 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_000009985.1:WP_011382998.1 Length = 400 Score = 194 bits (494), Expect = 3e-54 Identities = 122/365 (33%), Positives = 189/365 (51%), Gaps = 15/365 (4%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G +++ L G+PDFDTP I AA ++ G T Y G LRQ IA + +R +G Sbjct: 30 GRDVIGLGAGEPDFDTPDNIKAAAKAAIDKGLTKYGPPAGTVDLRQAIAAKFKRENGLDY 89 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 A+QV V G + ++ +NPGDEVIV P +V+Y + G + V VP G Sbjct: 90 TADQVTVGVGGKGVIFNAFMATINPGDEVIVPAPYWVSYPDIALMFGGKPVFVPCPETAG 149 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYSE 209 F++Q ++ ITPRT+ + LNSP NP+GA+ +AL ++ + H +W++SD++Y Sbjct: 150 FKLQPADLEKAITPRTKWLVLNSPSNPTGAAYSWDEMKALTDVLLRHPHVWIMSDDMYEH 209 Query: 210 LLFDG-EHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCML 267 L++D + +PA + P + DRT T+N +SK++AMTGWRVG+ GPAA+ + + + Sbjct: 210 LVYDDFKFCTPAQVEPKLYDRTLTMNGVSKAYAMTGWRVGYAAGPAAIIKAINMIQSQSV 269 Query: 268 YGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVD 327 + Q A+ AL + ++RRRDL++ L PG+ P+G +V Sbjct: 270 THTSSISQAASVEALNGTQDFIPKNAAVFKRRRDLIVGLLNQCPGITCRTPEGAFYVYPS 329 Query: 328 I-------RPTG---LSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLRE 377 P G + F LL+ GV+V+ G AFG + R+ L + Sbjct: 330 CAGVIGKKTPDGKVIANDTDFVGALLEAEGVAVVQGAAFG--LEPYFRISYATSDAALTK 387 Query: 378 ACRRI 382 A RI Sbjct: 388 AAERI 392 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: 21 Number of successful extensions: 4 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