Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_174545208.1 HTA01S_RS19080 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_001592305.1:WP_174545208.1 Length = 456 Score = 233 bits (595), Expect = 7e-66 Identities = 151/432 (34%), Positives = 230/432 (53%), Gaps = 20/432 (4%) Query: 3 KTNESL-LKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHP 61 K E+L L R ++ RG G++ PVV +RA T+ D +G +ID + G+ V + G HP Sbjct: 26 KAQEALALSARTESMARGGGRM-PVVMDRAFGVTIKDPDGNTFIDLSAGVGVSSVGRCHP 84 Query: 62 KVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKK--TLLVTSGSEAVENA 119 KV+ A+ +Q G L H + ELA +I++ +P T SGS+A+E A Sbjct: 85 KVVEAIHQQSGVLMHA--MEVNSTKRTELAAKISEIMPEGLRGDCITFFAQSGSDALEAA 142 Query: 120 VKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCEL--- 176 VK A+ TGR +IAF G YHG + LT Y G G GG+ A P Sbjct: 143 VKFAKRVTGRHQIIAFHGGYHGVWNASNALTTGTA-YRKGYGPFMGGVIHAPYPYAYRFP 201 Query: 177 ----HGVSEDDSIASIERIFKND-AQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCD 231 H +E + ++ + D+AA+I+EPVQGEGG+ S F+Q LR CD Sbjct: 202 FDTTHKSAEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQLLRKACD 261 Query: 232 QHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIA 291 + G LLI DEVQ GAGRTG +A E G+ PD+ TF K +GG P++G+ ++++ I Sbjct: 262 KSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGMGGDVPMAGLVMRSDLAAKIP 321 Query: 292 PGGLGGTYAGSPIACAAALAVLKVFEEEK--LLERSQAVGERLKAGLREIQAKHKVIGDV 349 G + T+A + ++ A AL + + ++ + LL R+ +G + +R + +G+V Sbjct: 322 DGSVPNTFAANSLSAAVALTNIGLLQDPELDLLNRAHQLGLEAQEYIRGF--NNPYVGEV 379 Query: 350 RGLGSMVAIELFEGGDTHKP-AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPD 408 RG G M+ IEL E T +P + E + K++ G++++ CG Y NV+R + +TIP Sbjct: 380 RGRGLMIGIELVEDKATKEPLSGEKLGKLMGYVLSHGVLMVPCGRYTNVMRVMPSLTIPR 439 Query: 409 AQLEKGLAILAE 420 L K L + E Sbjct: 440 KLLFKALDVFGE 451 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: 485 Number of extensions: 28 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: 426 Length of database: 456 Length adjustment: 32 Effective length of query: 394 Effective length of database: 424 Effective search space: 167056 Effective search space used: 167056 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 Apr 09 2024. 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