Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase
Query= BRENDA::Q88RB9 (425 letters) >FitnessBrowser__Marino:GFF3915 Length = 422 Score = 187 bits (476), Expect = 4e-52 Identities = 138/407 (33%), Positives = 213/407 (52%), Gaps = 19/407 (4%) Query: 25 PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTK--VSHTCFQ-V 81 P+ + AKN+ + +G+E +DF G LN GH + + A+ E + VS Sbjct: 19 PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78 Query: 82 LAYEPYVELCEKINKLVPGDFDKKTLLV-TTGSEAVENAVKIARAATGRAGVIAFTGGYH 140 A ++E +K + L P D K TG+ VE A+K+AR GR+G+I+FT G+H Sbjct: 79 TAKHDFMESYKK-HILDPRGLDYKMQFTGPTGTNCVEAALKLARKVKGRSGIISFTNGFH 137 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDAEPRD 200 G TM + TG + G+G G + + L G VD +A ++++ + + + Sbjct: 138 GVTMGAVATTGNK-HHRGGVGTPLGNVDFMFYDGYL-GDDVD-TLAIMDKLLSDGSSGFE 194 Query: 201 I-AAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMG 259 + AA+I+E VQGEGG E +K L LC +H ILLI D++Q G GRTG FF+ E G Sbjct: 195 LPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFAG 254 Query: 260 VAPDLTTFAKSIAG-GFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVIE-VFE 317 + PD+ T +KS++G G P+A V K E +D PG GT+ G+ +A A A +E ++ Sbjct: 255 IKPDIVTVSKSLSGYGLPMALVLFKPE-LDVWDPGEHNGTFRGNNMAFITARAAVENYWK 313 Query: 318 EEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVV 377 ++ + KA E L L+ I KYP ++G G M +G +A G + Sbjct: 314 DDAFANEVKAKTEVLGDALQSICDKYPGQFKMKGRGLM-------RGIEAKHADITGPIT 366 Query: 378 AKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424 +A E GLI+ + G V++ L+PLT + L KG A++ + EI Sbjct: 367 KRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEI 413 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: 466 Number of extensions: 25 Number of successful extensions: 5 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: 422 Length adjustment: 32 Effective length of query: 393 Effective length of database: 390 Effective search space: 153270 Effective search space used: 153270 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