Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate WP_086509625.1 BZY95_RS09090 aspartate aminotransferase family protein
Query= BRENDA::Q9I6J2 (456 letters) >NCBI__GCF_002151265.1:WP_086509625.1 Length = 446 Score = 277 bits (709), Expect = 4e-79 Identities = 161/442 (36%), Positives = 243/442 (54%), Gaps = 25/442 (5%) Query: 19 DHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAA 78 D + P+T +Q ++ RII AEG Y D++G +I D ++GLW G+ R E+ +A Sbjct: 17 DAYWMPYTGNRQF-KRDPRIIVGAEGSYFTDADGRRIFDGLSGLWTCGAGHCRPEITEAV 75 Query: 79 TRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYW 138 TRQ+++L Y+ FQ HP ELA I + P+G++HVF+TGSGSE+ DT L++ R YW Sbjct: 76 TRQLQQLD-YSPAFQFGHPKAFELAHRIRGLMPQGLDHVFYTGSGSESADTALKIARAYW 134 Query: 139 ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKA---LHEQGDFPIPGIVHIAQPYWYGEG 195 KG+P K ++GR GYHG G+SLGG+ A L QG H+ Sbjct: 135 RKKGKPTKTKLVGRAKGYHGVNFGGISLGGIGANRVLFGQGI----DADHLPHTLLAENA 190 Query: 196 GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKY 255 E G AE+L + I N+AA I EP+ G+ GVI PP Y ++REI ++ Sbjct: 191 FTKGMPERGAERAEELLELIALHDASNIAAVIVEPLAGSAGVIPPPKGYLQRLREICDQH 250 Query: 256 DILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQ 315 DIL I DEVI GFGR G G++ +G PD++ +AK LT+G +PMG V+V+ EI + Sbjct: 251 DILLIFDEVITGFGRMGSMTGAEEFGVVPDILNVAKQLTNGAVPMGAVIVQGEIYHTFME 310 Query: 316 GG------EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADH 369 G E HG+TYSGHPVA A AL + +L +++I++V+ E +P ++ L Sbjct: 311 HGGPDYMLELPHGYTYSGHPVACAAALAALDVLENDRLIQRVR-EMSPVFEEALHGLKGT 369 Query: 370 PLVGEARGVGMVAALEL--VKNKKTRERFTDKGVGMLCREHCFRNGLIMRAVGDTMIISP 427 + + R G+ AL++ + R F + M C+ G +R GDT+ + Sbjct: 370 RYISDIRNYGLAGALQIEPYPGEPARRPFE---IAM----KCWNKGFYVRYGGDTIQLGL 422 Query: 428 PLVIDPSQIDELITLARKCLDQ 449 P +++ +ID L+ + + + Sbjct: 423 PFIVERDEIDRLVNALGEAISE 444 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: 631 Number of extensions: 36 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: 446 Length adjustment: 33 Effective length of query: 423 Effective length of database: 413 Effective search space: 174699 Effective search space used: 174699 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 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