Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_012278671.1 SHAL_RS18655 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000019185.1:WP_012278671.1 Length = 405 Score = 223 bits (568), Expect = 8e-63 Identities = 143/397 (36%), Positives = 210/397 (52%), Gaps = 34/397 (8%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85 V+ R E S VWD EG+EYIDFAGGIAV GH HP ++ A++ Q KL H V+ E Sbjct: 25 VIPVRGEGSRVWDQEGKEYIDFAGGIAVNCLGHCHPALVGALKTQGEKLWHLS-NVMTNE 83 Query: 86 PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA-ATGRAG-----VIAFTGAY 139 P +ELA K V F ++ SG+EA E A+K+ R A + G +IAF A+ Sbjct: 84 PALELA---TKLVEATFAERVYFANSGAEANEAALKLVRRYAMDKFGAEKDQIIAFDKAF 140 Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199 HGRT T+ + G+ YS G G P I + I ++E +F + Sbjct: 141 HGRTFFTVSVGGQAA-YSDGFGPKPQSITHV----------PFNDIEALEAVFSDKT--- 186 Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259 A+++EP+QGEGG F++ +RALCD+H LL+ DEVQTG GR G +A + Sbjct: 187 --CAVMMEPLQGEGGIIDADPEFLKAVRALCDKHNALLVFDEVQTGVGRLGELYAYMRGD 244 Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319 +VPD+ T AK++GGGFPI+ + EI + G G TY G+P+ACA AV+ V Sbjct: 245 VVPDVLTTAKALGGGFPIAAMLTTKEIAAHLKIGTHGSTYGGNPLACAVGNAVMDVVNTP 304 Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVV 379 ++L + + + GL +I K+ V ++RG G ++ G + + +V Sbjct: 305 EVLNGVKHREQLFRDGLNKINDKYDVFSEIRGQGLLI------GAVVNSKYQGRAKEFLV 358 Query: 380 RAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLA 416 +G++ L G NV+RF + IP+ + +GLA Sbjct: 359 AGINEGVMSLVAGA--NVVRFTPSLVIPETDIAEGLA 393 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: 402 Number of extensions: 19 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: 405 Length adjustment: 31 Effective length of query: 395 Effective length of database: 374 Effective search space: 147730 Effective search space used: 147730 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 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