Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 399 bits (1026), Expect = e-116 Identities = 205/383 (53%), Positives = 258/383 (67%), Gaps = 1/383 (0%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MR+S T RI GD AAWDIH+ A +GE++++LSVGDPDFDTPAP+ AAI +L A Sbjct: 1 MRFSSLTDRIRGDRVAAWDIHFAAWTAKGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHA 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G+THY + G+ LR +A RR+G V+ E V+V AGAQ L+ CL+ GDEV+ Sbjct: 61 GDTHYTPIPGRPELRAALARDVARRTGLPVEPENVIVCAGAQNGLFNATLCLVEAGDEVL 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 V EPMY+TYEA A GA +VPV + R+ +AA +TPRTRA+ L +P NP+G Sbjct: 121 VPEPMYLTYEACVRASGATLVPVAPDAAT-LRLDPAALAAAVTPRTRAIFLATPANPTGI 179 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHA 240 + EA+A+L HDLW+++DEVY+ L FD H+ A+LPGMA+RT T+NSLSKSHA Sbjct: 180 VMSAEELEAVADLARRHDLWVVADEVYASLTFDRPHIGIATLPGMAERTVTINSLSKSHA 239 Query: 241 MTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRR 300 MTGWR GWVV PA L AH+ LALCMLYG P F+Q AA A+E + AMRE YRRRR Sbjct: 240 MTGWRAGWVVAPAPLVAHMGTLALCMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRR 299 Query: 301 DLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 D+ +E L PGLR L+P+ GMF++VD+R TGL FA RL GVSVL AFGP+A Sbjct: 300 DIALEALGSVPGLRCLKPEAGMFMLVDVRGTGLPTMEFAWRLFRETGVSVLDAGAFGPAA 359 Query: 361 AGHIRLGLVLGAEPLREACRRIA 383 AG +RL + L EACRRIA Sbjct: 360 AGCVRLSFAVSEAELAEACRRIA 382 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: 571 Number of extensions: 21 Number of successful extensions: 2 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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