Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate HSERO_RS20590 HSERO_RS20590 enoyl-CoA hydratase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__HerbieS:HSERO_RS20590 Length = 686 Score = 393 bits (1010), Expect = e-113 Identities = 231/521 (44%), Positives = 310/521 (59%), Gaps = 12/521 (2%) Query: 4 LLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYA 63 LL++ +AG+W+ G L V G A+ E +D A AR+ G AL AL + Sbjct: 7 LLQSFIAGRWL-GQRPSQALHSAVNGSAVASTHEESIDFGEALEHARKTGLPALMALDFQ 65 Query: 64 QRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGAS-LGEV 122 QRAA L + K L + YA++ A++G TR DS +DI+GG TL YA +GA+ Sbjct: 66 QRAAILKALAKYLMEHKEVLYAVS-AHTGATRADSWIDIEGGSGTLFTYASIGANEFPSS 124 Query: 123 HALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVK 182 + + +G A L K F+ H+L P GVA+ INAFNFP WG+ EK AP L+G+P IVK Sbjct: 125 NLVHEGPAMRLGKQGRFAGTHILVPRGGVAVHINAFNFPVWGMLEKFAPTFLAGMPCIVK 184 Query: 183 PATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLR 242 PATAT++L + V + +G+LP G+L ++ GS+ LL+++++ DVV+FTGSADTAA LR Sbjct: 185 PATATSYLAEAAVRLIQQSGLLPEGSLQLVIGSTGDLLERLQAQDVVTFTGSADTAAKLR 244 Query: 243 AHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRA 302 AHP + N EADSLN AIL D T D FDLF+KEV REMT K+GQKCTAIRRA Sbjct: 245 AHPNLIANSIPFNAEADSLNCAILGPDITADDEEFDLFVKEVAREMTTKAGQKCTAIRRA 304 Query: 303 FVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAY 362 VP ++ V E L A+L+KI VG+P + VRMG L SR Q +V +A LR A L Sbjct: 305 IVPRRHVDAVAERLAARLSKIVVGDPALETVRMGPLASRAQQRDVEERVALLRHSADLIL 364 Query: 363 DS-SAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALP 421 + SA A AP L + D + +H+VE FGPV+++ PY + L Sbjct: 365 GAGSAFAPQGQGVGEGAFFAPTLLLARDTAAGSPVHEVEAFGPVSTLMPY------DDLD 418 Query: 422 EAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMP 481 E A+ALA RG+GSLVAS+ + A R A HGR+ + TGHG+ +P Sbjct: 419 E--ALALAARGRGSLVASLVTRTPAVAARAIPVAAAWHGRLLVLDREAAAESTGHGSPLP 476 Query: 482 MSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTL 522 HGGPGRAGGGEELGG RA+ Y +R+A+Q + + + Sbjct: 477 QLKHGGPGRAGGGEELGGSRAVKHYLQRTAVQGSPTMLAAV 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: 770 Number of extensions: 33 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: 531 Length of database: 686 Length adjustment: 37 Effective length of query: 494 Effective length of database: 649 Effective search space: 320606 Effective search space used: 320606 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