Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Synpcc7942_1794 Synpcc7942_1794 succinyldiaminopimelate transaminase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__SynE:Synpcc7942_1794 Length = 392 Score = 147 bits (371), Expect = 5e-40 Identities = 108/359 (30%), Positives = 166/359 (46%), Gaps = 5/359 (1%) Query: 28 VEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTH-YADVRGKRALRQRIAERHRRRS 86 + G E++ LS+G D P +V SL +TH Y +G RQ A + R+ Sbjct: 29 IAAGREVIDLSLGSSDLPAPDHVVAVIAASLQDPSTHGYLLHQGTLPFRQVAAAWYERKF 88 Query: 87 GQAVDAE-QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPV 145 G VD E +V++L G+Q + ++ PG+ ++ +P Y ++ G + +P Sbjct: 89 GLGVDPETEVLLLIGSQEGTAHLPLAVMEPGEIALLQDPGYPSHAGGVYLAGGEIYRLPT 148 Query: 146 RSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDE 205 ++ GF + I R+R + L+ PHNP+ A P A +E C H L + D Sbjct: 149 TADRGFLPDFSTIPTEILSRSRLLVLSYPHNPTTAIAPLAFFEEAVAFCRHHQLVLAHDF 208 Query: 206 VYSELLFDGEHV-SPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLAL 264 Y +L FDG V S + SLSKS+ M G+RVG+ +G A L L L Sbjct: 209 PYPDLGFDGVEVPSIFQADRQKQQAIEFFSLSKSYNMGGFRVGFAIGNAELIGALRRLKA 268 Query: 265 CMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFV 324 + + + I A AL P +EA R+ +R RRD+ I LA + P +P M++ Sbjct: 269 VVDFNQYQGILAGAIAALTGPQACVEATRQRFRDRRDIFINALAATGWTIP-KPVSTMYL 327 Query: 325 MVDI-RPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRI 382 + P + F ++L+ GV+ G FG G +R LV + L EA RRI Sbjct: 328 WAPLPEPWQTRSLEFCEKLVAETGVAASPGIGFGDCGEGFVRFALVHDRDRLEEAARRI 386 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: 338 Number of extensions: 13 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: 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