Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_013459726.1 SULKU_RS04380 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= BRENDA::P42588 (459 letters) >NCBI__GCF_000183725.1:WP_013459726.1 Length = 431 Score = 172 bits (435), Expect = 3e-47 Identities = 123/402 (30%), Positives = 201/402 (50%), Gaps = 41/402 (10%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAK-QPLHSQELLDPLRAMLAKTLA 134 L D +G ID + + + GH NP + ++ QL + + L++ L Sbjct: 40 LEDFEGNRIIDAISSWWVNLFGHCNPYINRKIKEQLESLEHVILAGFTHEGIVRLSERLV 99 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG--KFTFIATSGAFHGKSLGALSATA 192 AL+P L F+ ++G+ ++E ALK++ RG + F++ + ++HG++LGALS Sbjct: 100 ALSPEGLTRCFYADNGSSAIEVALKMSYHSHKNRGEERGLFVSLTDSYHGETLGALSVGD 159 Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECK-------KTGDDVAAVILEP-IQGEG 244 + +++ + PLL +++ AL K + G ++AA+I+EP +QG G Sbjct: 160 VALYKETYEPLLIRSIQTLSPRDQSIEAALEAAKSFEILLQERGKEIAALIVEPLVQGAG 219 Query: 245 GVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGG 304 G+ + P +L+ ++LC+E+G I DE+ G GRTG MFACE + PD L L+K L G Sbjct: 220 GMKMYHPAFLSETKRLCEEYGIHFIADEILVGFGRTGSMFACEQAQITPDFLVLSKGLTG 279 Query: 305 GVMPIGATIATEEVFSVLF--DNP---FLHTTTFGGNPLACAAALATINVLLEQN----- 354 G +P+ + TE V+ + NP FLH+ ++ GN LACAAA AT+++ +N Sbjct: 280 GYLPLSVVLTTESVYGSFYCDYNPVRSFLHSHSYTGNALACAAANATLDIFESENVIENN 339 Query: 355 ---LPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNE----IGYNFASE 407 + A AE+ L F+ L + V+E R GM+ AIE + E IG Sbjct: 340 RKTIAAMAEE-----LKRFKSLPK-----VKEVRQCGMIAAIEVEEFEPHERIGLKIHRL 389 Query: 408 MFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKAL 449 Q VL+ I + P +T ++ + V A AL Sbjct: 390 CMEQGVLIRPL---GSVIYVMTPYVITPDELKSVFDAIESAL 428 Lambda K H 0.320 0.135 0.393 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: 433 Number of extensions: 23 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: 459 Length of database: 431 Length adjustment: 32 Effective length of query: 427 Effective length of database: 399 Effective search space: 170373 Effective search space used: 170373 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