Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Pf1N1B4_5070 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5070 Length = 404 Score = 224 bits (570), Expect = 4e-63 Identities = 141/395 (35%), Positives = 209/395 (52%), Gaps = 17/395 (4%) Query: 8 QRIAG-DGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYA 66 QR+A +A + I R R QG +I+ L G+PDFDTP + +AAI ++ G+T Y Sbjct: 10 QRLASAQPSATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHVREAAIHAIEHGHTRYT 69 Query: 67 DVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMY 126 V G R+LR+ +A + RR +G V + +V G + +Y + LN GD+VIV P + Sbjct: 70 QVAGVRSLREAVAAKFRRENGLDVSWQDTLVCNGGKQVIYNALAATLNEGDQVIVPAPYW 129 Query: 127 VTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRAT 186 V+Y + CG V ++ GF++ +AA ITP+TR + LNSP NP+GA Sbjct: 130 VSYPEMVQLCGGEARIVTCDADTGFKLTPAALAAAITPQTRWLILNSPSNPTGAVYSETE 189 Query: 187 WEALAELCMAH-DLWMISDEVYSELLFDGE--HVSPASLPGMADRTATLNSLSKSHAMTG 243 ALA + + H + +++D++Y L+FD + + P +A RT T+N +SK++AMTG Sbjct: 190 LRALAAVLLDHPHVLILADDIYEHLIFDDQAFYTLAQVEPRLAPRTLTMNGVSKAYAMTG 249 Query: 244 WRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLV 303 WR+G+ GP L +E L G+ Q AA ALE P + R A++ RRDL+ Sbjct: 250 WRIGFATGPRWLLEAMEKLQGQQTSGASSVSQQAALAALEGPKDFIRESRAAFQARRDLM 309 Query: 304 IECLADSPGLRPLRPDGGMFVMVD-IRPTGLSAQA---------FADRLLDRHGVSVLAG 353 + L D+PGL + P G + R G ++ A A LLD V+V+ G Sbjct: 310 VTLLNDTPGLECVSPAGAFYAFASCARLIGRTSPAGRVLHTDEDVAHALLDEADVAVVHG 369 Query: 354 EAFGPSAAGHIRLGLVLGAEPLREACRRI-ALCAA 387 AFG +IR+ L LR+AC I A C A Sbjct: 370 SAFG--LGPYIRIAYALDDASLRQACEAIRAFCTA 402 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: 488 Number of extensions: 28 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: 404 Length adjustment: 31 Effective length of query: 362 Effective length of database: 373 Effective search space: 135026 Effective search space used: 135026 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