Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 223 bits (569), Expect = 6e-63 Identities = 148/405 (36%), Positives = 217/405 (53%), Gaps = 34/405 (8%) Query: 27 VAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEP 86 V +R S VWD +GR+YIDFAGGIAV GH HP+++ + EQ GKL H EP Sbjct: 25 VPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHIG-NGYTNEP 83 Query: 87 YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR-AATGRAG-----VIAFTGAYH 140 + LA+ + F + SG+EA E A+K+AR A R G +I+FT ++H Sbjct: 84 VLRLAKRLEDLT---FADRAFFANSGAEANEAALKLARRVAFDRHGADKYEIISFTQSFH 140 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQD 200 GRT T+ + G+ YS G G +P GI H D IE + K A Sbjct: 141 GRTFFTVSVGGQP-KYSEGFGPVPAGI--------THLPYND-----IEAVKK--AIGAQ 184 Query: 201 IAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGI 260 A+I+EP+QGEGG +F++ LR CDQHG LLI DEVQTG GR+G F+A ++ G+ Sbjct: 185 TCAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGV 244 Query: 261 VPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEK 320 PD+ T AK++G GFPI + E+ G G TY G+P+ A A V+++ + K Sbjct: 245 TPDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPK 304 Query: 321 LLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVR 380 LLE ++ E LK L ++ + + +VRG G ++ EL + K A+ V Sbjct: 305 LLEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAEL---NEAFKGRAK---DFVTA 358 Query: 381 AREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425 A + G+I+L G +V+RF+ + +P + +G LA+ + + Sbjct: 359 AGQHGVIMLMAGP--DVLRFVPSLIMPLDDMNEGFERLAKAIESI 401 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: 432 Number of extensions: 17 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: 426 Length of database: 411 Length adjustment: 32 Effective length of query: 394 Effective length of database: 379 Effective search space: 149326 Effective search space used: 149326 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