Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 226 bits (575), Expect = 2e-63 Identities = 137/421 (32%), Positives = 213/421 (50%), Gaps = 13/421 (3%) Query: 39 ITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPF-YNLFFQTAHP 97 ++ A+GVY+WD G + LD +G N+G+GR ++ +A Q+ + F Y F+ A Sbjct: 17 VSHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFENA-- 74 Query: 98 PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157 P V LAKA+ + + VFF SGSEA ++ L++ R Y+ +G+PQ++ + YH Sbjct: 75 PAVALAKALVGFTQQQLEKVFFVSSGSEAVESALKLARQYFVARGEPQRRRFVSLRPSYH 134 Query: 158 GSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPDEFGVWAAEQLEKKILE 217 GST+ + + G + L G + +A P +Y D I Sbjct: 135 GSTLGALGVTGYQPLEAPFRDIAIGSLKVAGPDFYRHD-DTDDGRHVARVLADTRAAIEA 193 Query: 218 VGEENVAAFIAEPIQGAG-GVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFG 276 G + +AAF+ EP+ GA G +Y IR + ++ L I DEV+ G GRTG WF Sbjct: 194 AGPDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRTGTWFA 253 Query: 277 SQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGEFYHGFTYSGHPVAAAVAL 336 Q+YG PDL+ AKGL +GY P+G V+ R +IVE + G F HG TY+G+P+A A L Sbjct: 254 YQHYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHGHTYAGNPLACATGL 313 Query: 337 ENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKKTRERF 396 + + EKI++ V A A P VG+ RG+G++ +ELV + ++ F Sbjct: 314 AVVEAIEREKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLWGVELVADAASKAPF 373 Query: 397 TDK-----GVGMLCREH---CFRNGLIMRAVGDTMIISPPLVIDPSQIDELITLARKCLD 448 + + L RE + + GD +I+PPL ID + EL+T + + Sbjct: 374 PAEQNRFARITALAREEGLLIYPRRTLDGIAGDHFLITPPLTIDAADTAELLTRLERAMQ 433 Query: 449 Q 449 + Sbjct: 434 R 434 Lambda K H 0.320 0.138 0.425 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: 517 Number of extensions: 24 Number of successful extensions: 6 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: 456 Length of database: 450 Length adjustment: 33 Effective length of query: 423 Effective length of database: 417 Effective search space: 176391 Effective search space used: 176391 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