Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >MicrobesOnline__882:208056 Length = 542 Score = 191 bits (484), Expect = 6e-53 Identities = 138/415 (33%), Positives = 215/415 (51%), Gaps = 35/415 (8%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 P + + A+ + + D +G Y+D + GH HP + A++ QL +++H+ L Sbjct: 84 PCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQLDRVAHSTLLGLGG 143 Query: 85 EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIA-----RAATG---RAGVIAFT 136 P IELA + P + SGS AVE A+KIA +A G R V+AF+ Sbjct: 144 TPSIELAARLTAIAPAGLTR-VFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFS 202 Query: 137 GAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAP----CELHGVSEDDSIA---SIE 189 AYHG T+ ++ L G + + L+ + RA AP C E +A +E Sbjct: 203 NAYHGDTIGSVSLGGMSLFHGIYGPLLFDPV-RAPAPHCYRCPADLRPETCGMACLGEVE 261 Query: 190 RIFKNDAQPQDIAAIIIEP-VQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGR 248 R+ ++ ++ A+++EP VQG G V + +++ LR LCD+HG+ ++ADEV G G+ Sbjct: 262 RLMRHHGH--ELCAVVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGK 319 Query: 249 TGTFFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDAIAPGGL-------GGTYA 300 TGT FA EQ G+VPD+ AK + GG+ P++ I D G G TY Sbjct: 320 TGTMFACEQEGVVPDMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFHGHTYT 379 Query: 301 GSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIEL 360 G+ +ACAAALA L VFEEE+ LE + ERL L + V GD+R +G M IEL Sbjct: 380 GNALACAAALASLDVFEEERTLETLRPRIERLATLLAPLNDLPHV-GDIRRVGVMTGIEL 438 Query: 361 FEGGDT---HKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 +T ++P + ++ + AR +G+I+ G +V+ + P++I + +LE Sbjct: 439 VADRETRTPYRPEERIGHRVTLEARRRGVIVRPLG---DVMVLMPPLSITETELE 490 Lambda K H 0.319 0.137 0.393 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: 550 Number of extensions: 29 Number of successful extensions: 6 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: 426 Length of database: 542 Length adjustment: 34 Effective length of query: 392 Effective length of database: 508 Effective search space: 199136 Effective search space used: 199136 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