Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate RR42_RS35145 RR42_RS35145 aldehyde dehydrogenase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Cup4G11:RR42_RS35145 Length = 514 Score = 663 bits (1710), Expect = 0.0 Identities = 341/522 (65%), Positives = 397/522 (76%), Gaps = 8/522 (1%) Query: 1 MTELLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRAL 60 MTELL N++ G+W AG+GAG TL+DPV G ALVRV + GLDLA F+FARE GGAALRA+ Sbjct: 1 MTELLSNYLGGRWQAGSGAGATLSDPVLGDALVRVDATGLDLAAGFAFAREQGGAALRAM 60 Query: 61 TYAQRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120 TY +RAA LA IVK+LQ R YY IATANSGT NDSAVDIDGGIFTL YAKLG +LG Sbjct: 61 TYRERAAMLAAIVKILQTNRDAYYEIATANSGTVHNDSAVDIDGGIFTLGTYAKLGDALG 120 Query: 121 EVHALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180 E L DG A L KD F +QHVL PTRGVAL INAFNFPSWGLWEKAAPALL+GVPVI Sbjct: 121 ERRYLIDGDAARLGKDPLFQSQHVLVPTRGVALLINAFNFPSWGLWEKAAPALLAGVPVI 180 Query: 181 VKPATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAAT 240 VKPATATAWLTQRMV DVVDAG+LPPGALS++CGS+AGLLDQ++ FDVVSFTGSA TAA Sbjct: 181 VKPATATAWLTQRMVRDVVDAGVLPPGALSVVCGSAAGLLDQLQPFDVVSFTGSAQTAAL 240 Query: 241 LRAHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300 +R+H A QR R+N+EADS+NSA+L + AFDL KE REMTVKSGQKCTAIR Sbjct: 241 IRSHAAVTQRSVRVNIEADSVNSALLLPGEAAGSEAFDLLAKEAAREMTVKSGQKCTAIR 300 Query: 301 RAFVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVL 360 R FVPEA +A+ A+LA++TVGNPR++AVRMG+LVSR Q +V G+ L+ +A + Sbjct: 301 RIFVPEALYGAAADAIGARLARVTVGNPRHEAVRMGALVSRAQLASVREGLGYLQAQAEV 360 Query: 361 AYDSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420 +D + L+DAD +A CV P L D A +HD EVFGPVA++ PYR D Sbjct: 361 LHDGATHALVDADPAVACCVGPTLLGARDAHAADRVHDTEVFGPVATLVPYRDNAD---- 416 Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480 A+AL RRGQGSLVAS+Y +D L + A+ELADSHGRVH ISP V TGHGNVM Sbjct: 417 ----ALALVRRGQGSLVASLYGSDADALAKAAVELADSHGRVHVISPDVAQLHTGHGNVM 472 Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTL 522 P SLHGGPGRAGGGEELGGLRAL FYHRRSA+QA+++ + L Sbjct: 473 PQSLHGGPGRAGGGEELGGLRALNFYHRRSAVQASTSVLAQL 514 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: 739 Number of extensions: 28 Number of successful extensions: 2 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: 514 Length adjustment: 35 Effective length of query: 496 Effective length of database: 479 Effective search space: 237584 Effective search space used: 237584 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: 52 (24.6 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