Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_036377222.1 MVAN_RS29065 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_000015305.1:WP_036377222.1 Length = 465 Score = 216 bits (551), Expect = 1e-60 Identities = 141/421 (33%), Positives = 208/421 (49%), Gaps = 16/421 (3%) Query: 39 ITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHPP 98 + A+G ++WD +GNK+LD + L N+G+ ++V A +Q +L + Q A+ Sbjct: 51 LVAADGCHVWDGQGNKLLDFSSMLVNTNIGHQHPKVVAAIAQQAAKL--CTVAPQHANAA 108 Query: 99 VVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYHG 158 E A+ IA+ P +N +FFT G++A + +RM R + + V+ R+ YHG Sbjct: 109 RSEAARLIAERTPGELNRIFFTNGGADAVEHAVRMARLHTG------RSKVLSRYRSYHG 162 Query: 159 STVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEGGDMSPD-EFGVWAAEQLEKKILE 217 T ++L G D GIVH P+ Y + E A L I Sbjct: 163 GTDTAINLTG-DPRRWPNDHGTAGIVHFFGPFLYRSQFHAGTEAEESERALAHLHDTIRM 221 Query: 218 VGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWFGS 277 G +AA I E I G G++VPP Y +R + +Y I+FIADEV+ GFGR+G+WF Sbjct: 222 EGPNTIAAIILESIPGTAGIMVPPPGYMAGVRALCDEYGIVFIADEVMAGFGRSGKWFSI 281 Query: 278 QYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGEFYHGFTYSGHPVAAAVALE 337 ++ PDL+ AKG+ SGY+P+GGV + I E + G TYSGHP+A A A+ Sbjct: 282 NHFDVVPDLLTFAKGVNSGYVPLGGVAISPAIAETFAHRA-YPGGLTYSGHPLATAAAVA 340 Query: 338 NIRILREEKIIEKVKAETAPYLQKRWQEL-ADHPLVGEARGVGMVAALELVKNKKTRERF 396 I + E+ I+E A + +EL A H VGE RG G+ A+ELV ++ TRE Sbjct: 341 TINTMAEDGIVENAARVGAEVIGPGLRELAARHRSVGEVRGAGVFWAVELVADQTTREPL 400 Query: 397 TDKGVGMLCRE----HCFRNGLIMRAVGDTMIISPPLVIDPSQIDELITLARKCLDQTAA 452 G C + GL+ A + + + PP I Q E + + K LD A Sbjct: 401 APYGSSSAAMNSVIAECKKLGLLPFANYNRIHVVPPCTITDEQAREGLAILDKALDVADA 460 Query: 453 A 453 A Sbjct: 461 A 461 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: 588 Number of extensions: 36 Number of successful extensions: 7 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: 465 Length adjustment: 33 Effective length of query: 423 Effective length of database: 432 Effective search space: 182736 Effective search space used: 182736 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