Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Keio:15866 Length = 406 Score = 217 bits (552), Expect = 6e-61 Identities = 143/397 (36%), Positives = 204/397 (51%), Gaps = 37/397 (9%) Query: 26 FYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQ 85 F R E + LWD +G+ Y DFA GIAV GH HP + +A+ Q +F HT Sbjct: 23 FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTG------N 76 Query: 86 GYVT--LAERINALVPIQGLNKTALFTTGAEAVENAIKIAR--AH----TGRPGVIAFSG 137 GY + L+ ++ +GAEA E A+K+AR AH + + G++AF Sbjct: 77 GYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136 Query: 138 AFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDID 197 AFHGRTL ++ G+ A Y F P P+DI HA A + +++ AL ID Sbjct: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPADIRHA----AYNDINSASAL----------ID 181 Query: 198 PARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSH 257 + A+IVEP+QGEGG A F++GLR +C++H +LI DEVQTG GRTG+++A H Sbjct: 182 DS-TCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240 Query: 258 HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIE 317 + V PDL+T AK+L GG P+ A+ G G TY GNPLA A A V+++I Sbjct: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300 Query: 318 EEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377 ++ E L +EVRGLG ++ GQ AK++ Sbjct: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQ-----AKQIS 355 Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAAL 414 A +AG+++L G GNV+RF L + + + L Sbjct: 356 QEAAKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGL 390 Lambda K H 0.321 0.136 0.400 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: 454 Number of extensions: 27 Number of successful extensions: 5 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: 423 Length of database: 406 Length adjustment: 31 Effective length of query: 392 Effective length of database: 375 Effective search space: 147000 Effective search space used: 147000 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