Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Burk376:H281DRAFT_02621 Length = 447 Score = 199 bits (507), Expect = 1e-55 Identities = 129/413 (31%), Positives = 206/413 (49%), Gaps = 40/413 (9%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPL-HSQELLDPLRAMLAKTLA 134 +VD+ G +ID GG + +GH +P V+ A+Q Q+ + P H+ LA L Sbjct: 24 IVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHTSFFTTEPAEALADLLI 83 Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSAT 191 P L + +F + G+E++EAALKLA+ Y +G + FIA ++HG +LGAL+ Sbjct: 84 EAAPRNLGHVYFVSGGSEAMEAALKLARQYFVEKGQPERRHFIARRQSYHGNTLGALAIG 143 Query: 192 AKSTFRKPFMPLLPGFRHVP----FGNIEAMRTALNECKKTGDDVAAVILE--------- 238 + R+PF+P+L HV + +A T ++ D++ A ILE Sbjct: 144 GNAWRREPFLPILIEAHHVTPCFAYREQQAGETDEAFAQRLADELEAKILELGAQSVAAF 203 Query: 239 ----PIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPD 294 + G + P Y +R +CD++G L+ILDEV +GMGRTG +FACE + V PD Sbjct: 204 VAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMSGMGRTGHLFACEEDGVSPD 263 Query: 295 ILCLAKALGGGVMPIGATIATEEVFSVLFDNP--FLHTTTFGGNPLACAAALATINVLLE 352 IL +AK LG G PIGAT+ + E+F+ + F H T+ G+ ACAAAL V+ E Sbjct: 264 ILAIAKGLGAGYQPIGATLVSNEIFNTIVGGSGFFQHGHTYIGHATACAAALEVQKVIAE 323 Query: 353 QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYN--------- 403 + L + +G+ L R+ +P + + RG+G+ +E V + Sbjct: 324 EQLLDNVKARGEQLRARLREWQANHP-FIGDVRGRGLFTGVELVQDRASKTAFDPKHKLH 382 Query: 404 --FASEMFRQRVLV---AGTLNN--AKTIRIEPPLTLTIEQCELVIKAARKAL 449 SE ++ ++V GT++ + I PP T Q + +++ A+ Sbjct: 383 AIIKSEAMKRGLMVYPMGGTVDGRIGDHVLIAPPFITTSAQIDTIVERLADAI 435 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: 506 Number of extensions: 25 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: 459 Length of database: 447 Length adjustment: 33 Effective length of query: 426 Effective length of database: 414 Effective search space: 176364 Effective search space used: 176364 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