Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_085771871.1 B1812_RS12405 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_002117405.1:WP_085771871.1 Length = 398 Score = 202 bits (513), Expect = 2e-56 Identities = 140/390 (35%), Positives = 204/390 (52%), Gaps = 42/390 (10%) Query: 41 GREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKR-VP 99 G Y+DF G+AV + GH HP+++ A+Q+ + H Y+ I AE +A+R V Sbjct: 29 GGRYLDFGAGVAVNSLGHAHPRLLEALQQGATRPWHVSN---LYQ--IPQAERLAQRLVD 83 Query: 100 GDFPKKTLLVTSGSEAVENAVKIAR---AATG---RAGVIAFTGAYHGRTMMTLGLTGKV 153 F + L SG+EA+E A+K AR AA G R +I F GA+HGRT+ TL G Sbjct: 84 ASFADEVFLCNSGAEAIECAIKTARKFHAANGEPQRYRLITFEGAFHGRTLATLSAGGNR 143 Query: 154 VPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEG 213 Y G G P E + +A++E + + A ++IE +QGEG Sbjct: 144 -KYLDGFG----------PPVEGFDQAPFGDLAAVETLIGPET-----AGVLIESIQGEG 187 Query: 214 GFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGG 273 G V F++ LR LCDQ G+LL+ DEVQTG GR G+F A E+ G+ PD+ AK +GG Sbjct: 188 GIRVFPLEFLRALRTLCDQRGLLLVVDEVQTGVGRLGSFLAIERAGVSPDIAALAKGLGG 247 Query: 274 GFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLK 333 GFPI E + G G T+ G+P+A + A AVL V E LER + + L+ Sbjct: 248 GFPIGACLATKEAAKGMTLGAHGSTFGGNPLAASIANAVLDVVLSEGFLERVKRLEPVLR 307 Query: 334 AGLREIQAKH-KVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRAREKGLILLSCG 392 L E++ +H ++I +RG G M ++ T P E + AR+ GL+L++ G Sbjct: 308 QQLAELEDEHPQIIDSLRGEGLMFGLK------TRVPNLEFLK----AARDAGLLLVAAG 357 Query: 393 TYYNVIRFLMPVTIPDAQL-EKGLAILAEC 421 NV+R L P+ I ++ + E G + A C Sbjct: 358 D--NVVRLLPPLIIDESHIAEAGKRLRAAC 385 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: 421 Number of extensions: 18 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: 398 Length adjustment: 31 Effective length of query: 395 Effective length of database: 367 Effective search space: 144965 Effective search space used: 144965 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 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