Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_002968535.1 BIBO1_RS18510 aspartate aminotransferase family protein
Query= BRENDA::Q88RB9 (425 letters) >NCBI__GCF_000182725.1:WP_002968535.1 Length = 484 Score = 187 bits (476), Expect = 5e-52 Identities = 130/422 (30%), Positives = 208/422 (49%), Gaps = 43/422 (10%) Query: 24 HPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLA 83 H + V+ A+ D GR ++DF GG L GH HP+++AA ++ ++ H Sbjct: 61 HKVKVERAEGMYYYDQNGRRILDFFGGFGSLAFGHNHPRIIAARRKFQEELRHEIAIAFM 120 Query: 84 YEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATG--RAGVIAFTGGYHG 141 + L + PGD D L ++GSEA+E A+K+A A G + ++ +HG Sbjct: 121 SQYAAALAYDLAACSPGDLDM-VFLGSSGSEAMEAAIKVAERAAGPKKPKIVYAENSFHG 179 Query: 142 RTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDA-IASVERIFKNDAEPRD 200 +T L +T GG++R F + + V I ++E F++D E Sbjct: 180 KTKGVLSITD-------------GGLYRGEFKLVDNTVRVPFGDITAIENAFRSDPE--- 223 Query: 201 IAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGV 260 I I+LE VQG GG + A E ++LR LCD++G++ +ADEVQ G GRTG F+A E GV Sbjct: 224 IGTIVLETVQGGGGIIQADAEFWQKLRQLCDRYGVIWVADEVQCGFGRTGKFYAFEHYGV 283 Query: 261 APDLTTFAKSIAGG-FPLAGVCGKAE-YMDAIAPGGLG-----GTYAGSPIACAAALAVI 313 PD+T AKS+ GG +A + + + YM A T+ G AC A+ + Sbjct: 284 IPDVTALAKSLGGGKAAMAAMIARRDIYMKAYGTPKTAMIHAMATFGGIGEACITAIEAV 343 Query: 314 EVFEEEKLLDRSKAVGERLTAGLREIQKKYP-IIGDVRGLGSMIAVEVFEKGTHTPNAAA 372 + +E+L+D S VG+ L L+E+Q +YP ++ DVRG G M+ +E + P Sbjct: 344 NILYDEQLIDNSAEVGDYLLERLKELQVRYPGLLKDVRGKGMMVGLEFHDFSQAMPMVLR 403 Query: 373 VGQVVAKAREKGL--------------ILLSCGTYG-NVLRILVPLTAEDALLDKGLAII 417 + + KG +L++ Y NV+R+ PL + A +D+ + + Sbjct: 404 PMLAMLDDKLKGSLPGFIGSHLLRDHGVLVAFTEYNRNVIRLEPPLICQRAHVDEFIKAL 463 Query: 418 EE 419 +E Sbjct: 464 DE 465 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: 511 Number of extensions: 29 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: 484 Length adjustment: 33 Effective length of query: 392 Effective length of database: 451 Effective search space: 176792 Effective search space used: 176792 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 24 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