Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__WCS417:GFF1577 Length = 389 Score = 209 bits (532), Expect = 1e-58 Identities = 136/389 (34%), Positives = 202/389 (51%), Gaps = 35/389 (8%) Query: 30 RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89 R + +WD +GREY+D G+AV N GH HP+++AA+ EQ G L HT + + + Sbjct: 19 RGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTS-NLYSIDWQQR 77 Query: 90 LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAG-----VIAFTGAYHGRTM 144 LA+ + + D + SG+EA E A+K+AR + G V+ A+HGRT+ Sbjct: 78 LAQRLTQLSGLD---RAFFNNSGAEANETALKLARLHGWKKGIEAPLVVVMENAFHGRTL 134 Query: 145 MTLGLT-GKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAA 203 TL + G V G +PG + +A++E I K A I A Sbjct: 135 GTLAASDGPSV--RLGFQQLPGDFLKV----------RFGDLAALEAITK--AFGPRITA 180 Query: 204 IIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPD 263 +++EP+QGE G ++Q LR C + G L++ DE+QTG GRTGT+FA + GIVPD Sbjct: 181 VLLEPIQGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPD 240 Query: 264 LTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLE 323 + T AK +G G PI +A + PG G T+ G+P+AC VL + EE+ LL+ Sbjct: 241 VMTLAKGLGNGVPIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQ 300 Query: 324 RSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRARE 383 + GERL A LR +H + +RG G M+ IEL P +L + A+E Sbjct: 301 NAAQQGERLLARLRVELNEHAQVVAIRGQGLMIGIEL------ASPCRDLAQR---AAQE 351 Query: 384 KGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 GL++ T +IR L P+T+ ++E Sbjct: 352 HGLLINV--TRGKIIRLLPPLTLDTQEVE 378 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: 374 Number of extensions: 20 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: 389 Length adjustment: 31 Effective length of query: 395 Effective length of database: 358 Effective search space: 141410 Effective search space used: 141410 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