Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate PP_3270 PP_3270 oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Putida:PP_3270 Length = 684 Score = 373 bits (958), Expect = e-107 Identities = 221/522 (42%), Positives = 311/522 (59%), Gaps = 14/522 (2%) Query: 5 LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64 L++ +AG+W+ GA L + G L E D A A +AR G A+L + + Q Sbjct: 7 LQSFIAGRWLGQHGAQ-ALRSALDGHVLAYSHEERPDFAEAVDYARARGLASLMGMDFQQ 65 Query: 65 RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123 RA RL + L + YA++ +SG TR DS +DI+GG TL YA +G+ L + Sbjct: 66 RAQRLKALALYLAECKEQLYALSH-HSGATRADSWIDIEGGNATLFSYAGIGSRELPSGN 124 Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 + +G A L K F+ H+L P GVA+ INAFNFP WG+ EK AP L+G+P IVKP Sbjct: 125 LVHEGPAIPLGKQGHFAGSHILVPRAGVAVHINAFNFPIWGMLEKFAPTFLAGMPCIVKP 184 Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243 AT+T++LT+ +V + +G+LP G+L ++ GS+ LLD+++ DVV+FTGSADTAA LR Sbjct: 185 ATSTSYLTEAVVRLMNASGLLPEGSLQLVIGSTGDLLDRLQGQDVVTFTGSADTAAKLRV 244 Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 P ++ EADSLN AIL D +PD+ FDL+IKEVVREMT K+GQKCTAIRRA Sbjct: 245 TPNLIRNSVPFTAEADSLNCAILGPDVSPDSEEFDLYIKEVVREMTTKAGQKCTAIRRAI 304 Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAYD 363 VP L+ V L+ +L+K+ VG+P + VRMG+L S +Q +V + +L + + Sbjct: 305 VPARHLDAVATRLRERLSKVVVGDPSLEGVRMGALASHDQQRDVGERVRSLLQSCDQLFG 364 Query: 364 SS--AVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALP 421 +S P + A A AP L DP HD+E FGPV+++ Y + L Sbjct: 365 ASDGFAPRGEGVAE-GAFFAPTLLQARDPHAEGGAHDIEAFGPVSTLMAY------DDLD 417 Query: 422 EAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMP 481 E A+ALA RG+GSLVA++ + D + + A HGR+ + TGHG+ +P Sbjct: 418 E--ALALAARGKGSLVATLVTADRSVAAKAIPVAAAWHGRLLVLDSQAAKESTGHGSPLP 475 Query: 482 MSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLT 523 HGGPGRAGGGEELGGLRA+ Y +R+A+Q + + + +T Sbjct: 476 QLKHGGPGRAGGGEELGGLRAVKHYLQRAAVQGSPSMLTAVT 517 Lambda K H 0.318 0.132 0.379 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: 763 Number of extensions: 31 Number of successful extensions: 4 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: 531 Length of database: 684 Length adjustment: 37 Effective length of query: 494 Effective length of database: 647 Effective search space: 319618 Effective search space used: 319618 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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