Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate N515DRAFT_2186 N515DRAFT_2186 alanine-synthesizing transaminase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Dyella79:N515DRAFT_2186 Length = 410 Score = 143 bits (361), Expect = 8e-39 Identities = 114/374 (30%), Positives = 180/374 (48%), Gaps = 18/374 (4%) Query: 31 GEEILLLSVGDPD---FDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSG 87 G I+ L++G+P F+TP P ++ AI + L + Y +G R+ IA + R R Sbjct: 30 GLPIIKLNIGNPGRYGFETP-PHLRDAIAAHLRDSEAYGHEQGLEEARETIAAQQRARGA 88 Query: 88 QAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRS 147 + V+ E++ V G + ++ LL PGDEV++ P Y + A + + Sbjct: 89 RGVEVERIFVGNGVSELIDLSLRALLQPGDEVLLPSPDYPLWSAATILNDGQPRYYRCLA 148 Query: 148 ENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVY 207 ENG +E+ AL+T RTRA+ L +P+NP+GA PR E + + H L +++DE+Y Sbjct: 149 ENGHLPDPDEIEALVTARTRAIVLINPNNPTGAVYPRELLERIVRIAERHHLLLLTDEIY 208 Query: 208 SELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWV-VGPAALCAH-----LEN 261 E+L+DG P + + LSK H G+RVGW+ + + H L+ Sbjct: 209 DEILYDGAQFVPLATVAGDVPCVSFGGLSKVHRACGYRVGWMSLSGDPVRTHDYRDALQL 268 Query: 262 LALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRR---RRDLVIECLADSPGLRPLRP 318 LA L + Q A ALE+ P + A+ R R +++E +A+S L P Sbjct: 269 LAALRLCANVT-AQWAVRPALESK-PTIGALTSPGGRLHEARRMILEGVANSEFLDLATP 326 Query: 319 DGGMFVMVDIRPTGL---SAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPL 375 G ++ +R + AFA RLL+ V V+ G +F + H+RL L+ E L Sbjct: 327 GGALYAFPRVRADRVPRFDDNAFALRLLEEESVLVVPGSSFNVPDSRHLRLTLLPPPEQL 386 Query: 376 REACRRIALCAAEL 389 RE RI A + Sbjct: 387 REVFVRIERVLARM 400 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: 493 Number of extensions: 33 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: 410 Length adjustment: 31 Effective length of query: 362 Effective length of database: 379 Effective search space: 137198 Effective search space used: 137198 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