Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BWI76_RS07600 BWI76_RS07600 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >FitnessBrowser__Koxy:BWI76_RS07600 Length = 445 Score = 206 bits (525), Expect = 9e-58 Identities = 135/405 (33%), Positives = 205/405 (50%), Gaps = 22/405 (5%) Query: 38 IITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAHP 97 +I A+G +WD EGN LD + L VN+GY ++ A Q+ L + TA+ Sbjct: 38 VIAGAKGCELWDYEGNTYLDFSSQLVNVNIGYQHPRVLAAMKAQLEAL--VTIAPATANL 95 Query: 98 PVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGYH 157 E AK I ++APEG + VFFT +G++AN+ +RM R Y + V+ + YH Sbjct: 96 ARGEAAKRIVELAPEGFSKVFFTNAGADANENAIRMARLYTG------RDKVLSAYRSYH 149 Query: 158 GSTVAGVSLGG--MKALHEQGDFPIPGIVHIAQPYWY-GEGGDMSPDEFGVWAAEQLEKK 214 G+T + ++ G + +E G VH PY Y E + +E A L + Sbjct: 150 GNTGSAIAATGDWRRVPNEYSR----GHVHFFNPYLYRSEFNATTEEEECQRALAHLRRM 205 Query: 215 ILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEW 274 I G +AA + E I G G++VPP+ Y +R + ++ I+ I DEV+ GFGRTG W Sbjct: 206 IECEGPNAIAAILLESIPGTAGILVPPEGYMQGVRALADEFGIILILDEVMAGFGRTGSW 265 Query: 275 FGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGGEFYHGFTYSGHPVAAAV 334 F + G PDL+ AKG+ +GY+P GGV++ + I + F G TYSGHP+A A Sbjct: 266 FAFEQDGVVPDLVTFAKGVNAGYVPAGGVLISEPIARYFDD-HFFAGGLTYSGHPLAMAA 324 Query: 335 ALENIRILREEKIIEKVKAETAPYLQKRWQELAD-HPLVGEARGVGMVAALELVKNKKTR 393 + I ++EEK++E L+ + LA+ H ++G RG G+ ALELV +R Sbjct: 325 IVATIDAMKEEKVVENAATIGNEVLRPGLEALAEKHAIIGNVRGRGLFQALELV---SSR 381 Query: 394 ERFTDKGVGMLC--REHCFRNGLIMRAVGDTMIISPPLVIDPSQI 436 E T G + + GL+ V + + + PP I Q+ Sbjct: 382 EHKTPLGAADMAAIKGALTEAGLLAFVVENRIHVVPPCTISAEQV 426 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: 532 Number of extensions: 31 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: 456 Length of database: 445 Length adjustment: 33 Effective length of query: 423 Effective length of database: 412 Effective search space: 174276 Effective search space used: 174276 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 17 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