Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS07710 BPHYT_RS07710 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__BFirm:BPHYT_RS07710 Length = 487 Score = 556 bits (1434), Expect = e-163 Identities = 270/484 (55%), Positives = 349/484 (72%) Query: 3 LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62 L+I+G+W G G + NP +G +W+GN A A V++A R+AR AFP W+ LS ER Sbjct: 4 LFIDGEWAAGTGPAFASHNPGTGAAVWEGNSASADDVDRAVRSARRAFPAWSALSLDERC 63 Query: 63 AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122 VV RFAAL+ K L I RETGKP WEA TE +M K+ ISI+AY+ RTGE+RS Sbjct: 64 GVVRRFAALVTERKEALAEAIGRETGKPLWEARTEAASMAAKVEISIQAYNERTGEKRSA 123 Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182 M DG A LRHRPHGV+AVFGPYNFPGHLPNGHIVPAL+AGN ++FKPSEL P ++ Sbjct: 124 MADGTAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNAVVFKPSELAPGVAALTVQ 183 Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242 +W+ AGLP GVLNLVQG ++TG AL+ +DGL FTGS++TG LH+Q G+PE +LAL Sbjct: 184 IWRDAGLPTGVLNLVQGEKDTGIALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLAL 243 Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVS 302 EMGGNNPL+I VAD+DAAVH TIQSAF++AGQRCTCARR+ + + A GD F+ R V+ Sbjct: 244 EMGGNNPLVIGPVADVDAAVHHTIQSAFLSAGQRCTCARRIFVPNDAGGDRFMERFTEVT 303 Query: 303 QRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGI 362 R+T G ++ +PQPF+G +IS +AA ++V A ++L A G + LL +TP I Sbjct: 304 SRITVGEYNADPQPFMGAVISARAASRLVAAQERLLADGAKALLKMEQRDPKLGFVTPAI 363 Query: 363 IEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEA 422 +++T V +PDEE FGPL ++ RY +F+EA+ AN+T FGLS GL++ + + Sbjct: 364 LDVTNVKNLPDEEHFGPLAQIIRYGSFNEALEQANDTEFGLSAGLLADDEALWTHFQRTI 423 Query: 423 RAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNP 482 RAGIVNWN+P GA+S APFGG G SGNHRPSA+YAADYCA+PMAS+ES L +PA+++P Sbjct: 424 RAGIVNWNRPTNGASSGAPFGGPGRSGNHRPSAYYAADYCAFPMASVESAQLQMPASVSP 483 Query: 483 GLDF 486 GL F Sbjct: 484 GLQF 487 Lambda K H 0.318 0.134 0.412 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: 778 Number of extensions: 37 Number of successful extensions: 1 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: 492 Length of database: 487 Length adjustment: 34 Effective length of query: 458 Effective length of database: 453 Effective search space: 207474 Effective search space used: 207474 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 (21.7 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