Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Miya:8500245 Length = 491 Score = 193 bits (490), Expect = 1e-53 Identities = 138/429 (32%), Positives = 215/429 (50%), Gaps = 65/429 (15%) Query: 74 NTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQP------LHSQELLDPLRA 127 N L DT G ++D + GHR+P + +A++ QL K L S+ ++ Sbjct: 59 NRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGSEPSIE---- 114 Query: 128 MLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAY--QSPRG------KFTFIATSGA 179 LA LAA+ P L F+ +SG+ SVE ALK+A + Q+P + F++ A Sbjct: 115 -LAARLAAIAPQGLTRVFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFLSLRNA 173 Query: 180 FHGKSLGALSATAKSTFRKPFMPLL--------PGFRHVPFGNIEAMRTALNEC------ 225 +HG ++GA++ + F + PLL P PFG + EC Sbjct: 174 YHGDTVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAG--SCERECITHMET 231 Query: 226 --KKTGDDVAAVILEP-IQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGK 282 + G ++ A ++EP +QG G++L PPG+L VR+LCDE G ++ DEV G G+TG Sbjct: 232 LFARHGHELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVAVGFGKTGT 291 Query: 283 MFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFD-----NPFLHTTTFGGNP 337 +FACE E V PD LCLAK + GG +P+ AT+ TE V F H T+ GNP Sbjct: 292 LFACEQEGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTFFHGHTYTGNP 351 Query: 338 LACAAALATINVLLEQNLPAQAEQKGDML---LDGFRQLAREYPDLVQEARGKGMLMAIE 394 LACAAA+A+++V E+ + + + K L LD R L V + R +G++ IE Sbjct: 352 LACAAAIASLDVFEEERVMERLQPKIARLAARLDTLRDLPH-----VGDIRQRGVMTGIE 406 Query: 395 FVDN-----------EIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIK 443 V N +G+ E R+ V++ + + PPL++T ++ +L++ Sbjct: 407 MVRNRATKEAYDLALRVGHRVTLEARRRGVIIRPL---GDVMVLMPPLSITDDEIDLLVG 463 Query: 444 AARKALAAM 452 A +A+ A+ Sbjct: 464 ATGEAIRAV 472 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: 511 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: 491 Length adjustment: 33 Effective length of query: 426 Effective length of database: 458 Effective search space: 195108 Effective search space used: 195108 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