Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= BRENDA::Q97XA5 (470 letters) >MicrobesOnline__882:208821 Length = 464 Score = 245 bits (626), Expect = 2e-69 Identities = 151/462 (32%), Positives = 250/462 (54%), Gaps = 8/462 (1%) Query: 7 IEVRSPSNLKVIGTVKRMSKDEVRGEIEEAYKGF-EIISRMPLYKRTAILRKISEILERE 65 I VR+P +L +G V MS+ E +E A+ + R+P ++R AIL +++ ++ Sbjct: 4 ITVRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHRIPAHERLAILERLATLMRTH 63 Query: 66 QERLARLLAMEAGKPISDSRVEVLRASRLFRQAAEEVGIVLEGKNYRVDAYEYPPGNENR 125 E L R E GKP +DS VEV RA R AA E+ L G+ + P + R Sbjct: 64 AEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELA-QLGGREVPMGL---TPASAGR 119 Query: 126 IVLSTREPIGVVTAILPFNFPINSFAHKVAPALAVGNSVVVKPSINTPLAAVEMKKILVE 185 + + REP GVV AI FN P+N H+ PA A G V+VKP+ TPL+ + +++ E Sbjct: 120 LAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHE 179 Query: 186 AGLPDSAVRVVTGYSSEIGDEIITHPLVGLITLTGSTQTGLKIASKAISLGKRIIMELGG 245 AG+P++ ++ ++ ++++ P V ++ GS++ G + SK ++ G +E GG Sbjct: 180 AGVPEAWATMLP-CAAATAEKLVADPRVAFLSFIGSSRVGWHLRSK-LAPGATCALEHGG 237 Query: 246 SDPIIILEDANIERASSIAVRARFEYAGQNCNAGKRIIVRQEVYDKFVKAFNEKAKALKV 305 + P+++ A+++ A + ++ F +AGQ C + +R+ E F + A L Sbjct: 238 AAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPT 297 Query: 306 GEPLDETTDVGPVINKESVENLNSVLEDAKVKGGRVEILNRGPESGSFFPLTMVTNPSLD 365 G+P+ T VGP+I+ V ++ +E+A+ GG V + P S + + T+V +P Sbjct: 298 GDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTV-LCGGAPLSETLYSPTVVYDPPQG 356 Query: 366 MLVLKSEVFGPIVPIVSVKSDEEAIRIANSTEYGLQSAIFTNDVNRALKLSRELKFGAVI 425 + ++EVFGP+V + S + +EAI AN + Q+A+F DV+ AL +R L V+ Sbjct: 357 CRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVM 416 Query: 426 INDSTRLRWDSLPFGGFKKTGIGREGVRETMLEMTENKLIAI 467 +ND T R D +PFGG ++G+G G+ M EMT KLI + Sbjct: 417 VNDHTAFRVDWMPFGGRGESGMGTGGIGPAMHEMTTEKLIVL 458 Lambda K H 0.316 0.135 0.366 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: 403 Number of extensions: 14 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: 470 Length of database: 464 Length adjustment: 33 Effective length of query: 437 Effective length of database: 431 Effective search space: 188347 Effective search space used: 188347 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 (21.6 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