Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate H281DRAFT_00095 H281DRAFT_00095 beta-alanine--pyruvate transaminase
Query= BRENDA::Q88RB9 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_00095 Length = 443 Score = 171 bits (432), Expect = 5e-47 Identities = 142/430 (33%), Positives = 208/430 (48%), Gaps = 48/430 (11%) Query: 25 PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84 P + +AK +GR ++D G+ +N GH ++VAAVQ Q ++ + + Sbjct: 29 PRLLASAKGMYYTSHDGRRILDGTAGLWCVNAGHCRDEIVAAVQAQAAEMDFAPTFQMGH 88 Query: 85 EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARA---ATGRAGVIAFTG---G 138 E KI + PGD K V +GSEAV+ A+KIA A + G F G G Sbjct: 89 PKAFEAATKIARHTPGDL-KHIFFVNSGSEAVDTALKIALAYHRSRGEGQRTRFIGRERG 147 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSE---LHGISVDDAIAS-------- 187 YHG + + G A G AL PS H +++ +A S Sbjct: 148 YHGVGFGGISVGGIAPNRKAFSG--------ALLPSIDHLPHTLNIKEAAYSKGQPAWGA 199 Query: 188 -----VERIFK-NDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADE 241 +ERI +DA +AA+I+EPV G G L P+ ++RLR +CD+HGILLI DE Sbjct: 200 HLADELERIVALHDAST--VAAVIVEPVAGSTGVLIPPQGYLQRLREICDKHGILLIFDE 257 Query: 242 VQTGAGRTGTFFAMEQMGVAPDLTTFAKSI-AGGFPLAGVCGKAEYMDAI---APGGL-- 295 V TG GR G FA + GV PDL T AK P+ V + D+I APGG+ Sbjct: 258 VITGWGRLGAPFAAQYFGVTPDLLTMAKGTNNAAAPMGAVAASGQIHDSIVNGAPGGIEL 317 Query: 296 --GGTYAGSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLG 353 G TY+G PIA AAA A I+++E E+L D++ + + +++ + +I DVR LG Sbjct: 318 FHGYTYSGHPIAAAAACATIDLYEREQLFDQAARMAPLFERAIHKLRGERHVI-DVRNLG 376 Query: 354 SMIAVEVFEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKG 413 + VE+ + P A V + +KG++ G++L PL E+A +D+ Sbjct: 377 LVGGVELAPR-DGAPGTRAY-DVFVRCFQKGVLTRYT---GDILAFSPPLIIEEAQIDEI 431 Query: 414 LAIIEECFAE 423 A + E E Sbjct: 432 FATVAEVLRE 441 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: 514 Number of extensions: 28 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: 425 Length of database: 443 Length adjustment: 32 Effective length of query: 393 Effective length of database: 411 Effective search space: 161523 Effective search space used: 161523 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