Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Pf6N2E2_5269 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= BRENDA::Q88RB9 (425 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5269 Length = 416 Score = 349 bits (896), Expect = e-101 Identities = 173/414 (41%), Positives = 262/414 (63%), Gaps = 9/414 (2%) Query: 16 VPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVS 75 + + + +HP+ + KN+ V D +G+ IDF GGI VLN GH HP++V A++EQ T+++ Sbjct: 6 ISQSISIVHPVSLSHGKNAEVWDADGKRYIDFVGGIGVLNLGHCHPRIVEAIREQATRLT 65 Query: 76 HTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAF 135 H F + PY+EL E++ VP D+ +L +G+EA ENA+KI R ATGR VIAF Sbjct: 66 HYAFNAAPHTPYIELMERLAAFVPVDYPVSGMLTNSGAEAAENALKIVRGATGRTAVIAF 125 Query: 136 TGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKND 195 G +HGRT+ TL L GKV PY +G++PG ++ +PS+ +G++ ++A+ ++ER+F + Sbjct: 126 DGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVYHLPYPSKDNGVTREEALRAMERLFSVE 185 Query: 196 AEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAM 255 + D+A I+EPVQGE GFL + LR CD GI+LI DE+Q+G GRTG FA Sbjct: 186 IDVNDVACFIVEPVQGEAGFLAMDVLFAQALRQFCDDKGIVLIVDEIQSGFGRTGQRFAF 245 Query: 256 EQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIEV 315 ++G+ PDL KSIAGG PL V G+ +D + GGLGGTY+G+PIACAAALA ++ Sbjct: 246 SRLGIEPDLVLLGKSIAGGVPLGAVVGRKALLDNLPKGGLGGTYSGNPIACAAALATLDE 305 Query: 316 FEEEKLLDRSKAVGERLTAGLREIQKK--YPIIGDVRGLGSMIAVEVFEKGTH---TPNA 370 + L E + + + + + P +G + G+G+M +E+ TH TP + Sbjct: 306 MTDANLHAWGSQQEEAIVSRYQSWRNRGLTPYLGRLTGVGAMRGIEL----THADGTPAS 361 Query: 371 AAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424 A + Q++A ARE GL+L+ G +++R+L PLT E +L++GL I+E C A++ Sbjct: 362 AQLTQLLALARESGLLLMPSGKSRHIVRLLAPLTTEPNVLEEGLDILEACLAKL 415 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: 500 Number of extensions: 18 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: 425 Length of database: 416 Length adjustment: 32 Effective length of query: 393 Effective length of database: 384 Effective search space: 150912 Effective search space used: 150912 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: 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