Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_001294205.1:WP_053937056.1 Length = 400 Score = 236 bits (602), Expect = 9e-67 Identities = 144/409 (35%), Positives = 227/409 (55%), Gaps = 40/409 (9%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85 +V R S VWD G+EYIDF GGIAV + GH HP+++AA+ EQ KL H V E Sbjct: 21 IVPVRGAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHIS-NVFTNE 79 Query: 86 PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAAT------GRAGVIAFTGAY 139 P + LA+ + + F ++ SG+EA E A+K+AR A+ + V++ ++ Sbjct: 80 PALALAKTLVEHT---FAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSF 136 Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199 HGRT T+ + G+ YS G G P GI + + +AS+E + +D Sbjct: 137 HGRTFFTVSVGGQP-KYSDGFGPKPAGIEHF----------KYNDLASLEALIDDDT--- 182 Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259 A +IIEP+QGEGG ++ F+Q +RALCD+ LLI DEVQ+G GRTG+ +A G Sbjct: 183 --ACVIIEPIQGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFG 240 Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319 +VPD+ + AK +GGGFPI + ++ + G G TY G+P+A A A + + Sbjct: 241 VVPDILSTAKGLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAVAGTAISIITRP 300 Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSK--- 376 + L +A ER++AGL+ I K+ V+ ++RG+G ++ ++L AE + Sbjct: 301 ETLSGVKAKSERIRAGLQAIADKYPVVAEIRGMGLLIGVQL---------KAEYAGRSRD 351 Query: 377 IVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDEL 425 ++ A E+G+++L+ G +V+RF + I D +++ GLA + + F L Sbjct: 352 VLNAAAEEGVLVLAAGP--DVVRFAPSLVISDDEIDAGLARVEKAFARL 398 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: 419 Number of extensions: 22 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: 400 Length adjustment: 31 Effective length of query: 395 Effective length of database: 369 Effective search space: 145755 Effective search space used: 145755 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