Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q9I6J2 (456 letters) >MicrobesOnline__882:208056 Length = 542 Score = 221 bits (562), Expect = 6e-62 Identities = 133/444 (29%), Positives = 229/444 (51%), Gaps = 9/444 (2%) Query: 8 AKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNV 67 ++T ++L H PFT + II A+G ++ D++GN+ LD ++ LW NV Sbjct: 56 SRTARLRSLDAAHVWHPFTQMRDWMGSEPCIIDAADGNHLIDTDGNRYLDGVSSLW-TNV 114 Query: 68 GYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEAN 127 R + A R+ + ++ P +ELA + +AP G+ VF++ SGS A Sbjct: 115 HGHRHPHIDEAIRRQLDRVAHSTLLGLGGTPSIELAARLTAIAPAGLTRVFYSDSGSTAV 174 Query: 128 DTVLRMVRHYW--ATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVH 185 + L++ Y A +G ++ V+ N YHG T+ VSLGGM H + V Sbjct: 175 EAALKIAFQYHRQAPEGDARRTRVMAFSNAYHGDTIGSVSLGGMSLFHGIYGPLLFDPVR 234 Query: 186 IAQPYWYGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYW 245 P+ Y D+ P+ G+ ++E+ + G E A + +QGA G++V P + Sbjct: 235 APAPHCYRCPADLRPETCGMACLGEVERLMRHHGHELCAVVVEPLVQGAAGMLVQPRGWL 294 Query: 246 PKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVV 305 +R++ ++ + +ADEV GFG+TG F + G PD++ +AKG+T GY+P+ +V Sbjct: 295 RGLRDLCDRHGVFMVADEVAVGFGKTGTMFACEQEGVVPDMLCLAKGITGGYLPLAATLV 354 Query: 306 RDEIVEVLNQG----GEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQK 361 + I + G F+HG TY+G+ +A A AL ++ + EE+ +E ++ L Sbjct: 355 TEHIHDGFLGGYADFRTFFHGHTYTGNALACAAALASLDVFEEERTLETLRPR-IERLAT 413 Query: 362 RWQELADHPLVGEARGVGMVAALELVKNKKTRERF-TDKGVGMLCREHCFRNGLIMRAVG 420 L D P VG+ R VG++ +ELV +++TR + ++ +G R G+I+R +G Sbjct: 414 LLAPLNDLPHVGDIRRVGVMTGIELVADRETRTPYRPEERIGHRVTLEARRRGVIVRPLG 473 Query: 421 DTMIISPPLVIDPSQIDELITLAR 444 D M++ PPL I ++++ L+ R Sbjct: 474 DVMVLMPPLSITETELETLVHTVR 497 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: 647 Number of extensions: 37 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: 542 Length adjustment: 34 Effective length of query: 422 Effective length of database: 508 Effective search space: 214376 Effective search space used: 214376 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: 52 (24.6 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