Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate AO353_15915 AO353_15915 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15915 Length = 382 Score = 171 bits (433), Expect = 3e-47 Identities = 118/358 (32%), Positives = 184/358 (51%), Gaps = 13/358 (3%) Query: 37 LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE-QV 95 LS G PDFD P + A + G+ Y+ + G ALRQ++A + R G +V+A+ +V Sbjct: 29 LSQGFPDFDAPQALCDAVGRHIANGHNQYSPMTGLPALRQQVAAKIARSYGVSVNADTEV 88 Query: 96 VVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQA 155 + GA A++ + +++ GDEVIV +P Y +YE G R V VP+ ++ F + Sbjct: 89 TITPGATQAIFCAIAAVIHSGDEVIVFDPAYDSYEPSVALAGGRCVHVPLGGKD-FAIDF 147 Query: 156 EEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFDG- 214 +++ ++PRTR + LNSPHNPSGA + RA + LA L D+++ISDEVY L+FDG Sbjct: 148 QKLGEALSPRTRMIILNSPHNPSGALISRAELDQLAALIRDRDIYLISDEVYEHLVFDGV 207 Query: 215 EHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFI 274 H S + + R ++S K++ +TGW+ G+VV P AL L + + + + Sbjct: 208 AHASVLAHEELYQRAFVVSSFGKTYHVTGWKTGYVVAPPALTEELRKVHQYVSFCGVTPL 267 Query: 275 QDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVD---IRPT 331 Q A + +E + Y+ +RDL + LA S + G F +VD IRP Sbjct: 268 QYALADFMAEHPEHVEELPGFYQAKRDLFCDLLAPS-RFSFTKATGTYFQLVDYSQIRP- 325 Query: 332 GLSAQAFADRLLDRHGVSVLAGEAFGPSAAGH---IRLGLVLGAEPLREACRRIALCA 386 L+ A + HGV+ + F + +RL E LR+A + LCA Sbjct: 326 DLNDVEMAKWMTREHGVAAIPISVFYQNPLPEQRLVRLCFAKREETLRQAAEK--LCA 381 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: 401 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: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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