Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate AO356_27515 AO356_27515 4-aminobutyrate aminotransferase
Query= BRENDA::Q88RB9 (425 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27515 Length = 457 Score = 234 bits (598), Expect = 3e-66 Identities = 151/430 (35%), Positives = 230/430 (53%), Gaps = 23/430 (5%) Query: 3 KTNESL-MQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHP 61 +T E+L + R ++ RG G++ P+ +D A +T D + ID + G+ V + G HP Sbjct: 25 RTTEALALSARTESMARGGGRM-PVAMDRAFGATFKDADDNTYIDLSAGVGVSSVGRCHP 83 Query: 62 KVVAAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDF--DKKTLLVTTGSEAVENA 119 KVV A++EQ + H + EL K++++ P D T +GS+A+E A Sbjct: 84 KVVQAIREQSEVLMHAL--EVNSTRRTELAAKLSEIAPDGLRGDCITFFTQSGSDALEAA 141 Query: 120 VKIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGI 179 +K A+ TGR +IAF GGYHG + LT Y G G GG+ A +P + Sbjct: 142 IKFAKRVTGRHQIIAFHGGYHGVWNASGALTTGTA-YRKGYGAQMGGVIHAPYPYA-YRF 199 Query: 180 SVDDAIASVERIFKNDAE---------PRDIAAIILEPVQGEGGFLPAPKELMKRLRALC 230 D S E+I + D+AA+I+EPVQGEGG++P E ++ LR C Sbjct: 200 PFDTTHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQLLRKAC 259 Query: 231 DQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAI 290 D+ G LLI DEVQ+GAGRTG +A+E GV PD+ TF K I P+AG+ +++ AI Sbjct: 260 DRSGTLLIVDEVQSGAGRTGKMWAVEHSGVKPDMLTFGKGIGSDLPMAGLIMRSDLAAAI 319 Query: 291 APGGLGGTYAGSPIACAAALAVIEVFEEEK--LLDRSKAVGERLTAGLREIQKKYPIIGD 348 G + T+A + ++ A AL I + ++ + LL+R+ +G +R P++G+ Sbjct: 320 PDGSMPNTFAANSLSAAVALTNISILQDPELDLLNRAHTLGLEAQERIRGFGS--PLVGE 377 Query: 349 VRGLGSMIAVE-VFEKGTHTPNA-AAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAE 406 VRG G MI +E V + T P A +GQ++ G++++ CG Y NV+R++ LT Sbjct: 378 VRGRGLMIGIELVSDPTTKAPLAPEKIGQLMGYLLSHGVLMIPCGRYSNVMRVMPSLTIS 437 Query: 407 DALLDKGLAI 416 AL K L I Sbjct: 438 RALFFKALDI 447 Lambda K H 0.320 0.138 0.395 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: 528 Number of extensions: 35 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: 425 Length of database: 457 Length adjustment: 32 Effective length of query: 393 Effective length of database: 425 Effective search space: 167025 Effective search space used: 167025 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 (21.8 bits) S2: 51 (24.3 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