Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >FitnessBrowser__PS:Dsui_0437 Length = 483 Score = 310 bits (794), Expect = 7e-89 Identities = 172/479 (35%), Positives = 260/479 (54%), Gaps = 5/479 (1%) Query: 7 LLMLENFIGGKFLPCNSYIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSP 66 LL + ++ G+++ S ++P++G +VP G E AA+ AA A+PAW SR+ Sbjct: 8 LLRQQCYLNGQWVGGESDFPVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSRTA 67 Query: 67 QERSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVS 126 +ER+ VL R +++ Q ++LA + +QGK L AR ++ + +FA Sbjct: 68 KERTGVLRRWFELMNQHADDLALLMTSEQGKPLAEARG-EVAYAASFVEWFAEEAKRAYG 126 Query: 127 ECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVT 186 E ++ P+G+ I+PWN P ++T K+APA+AAG TV+ KP+E T +T Sbjct: 127 ETIPAVAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLT 186 Query: 187 AWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPH 246 A +L +AG P GV N++ G +G L S+P V +SFTGS + AP Sbjct: 187 ALALAELAHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPS 246 Query: 247 CKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKR 306 KKLSLELGG P I+F+DA+L+ + + S + N G+ C+C +R+ VQ IY F R Sbjct: 247 IKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEAFAAR 306 Query: 307 FVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLR 366 KVG ++ G LI L KV +++ A GAR+L G + Sbjct: 307 LAAKVATLKVGEGTEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHE----RY 362 Query: 367 NQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSK 426 + G F PTV+ D+ + R EE FGPV + F +EEE I AN+ +GLA+ +S+ Sbjct: 363 REGGAFFQPTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSR 422 Query: 427 DVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITI 485 D+GRI RV + L+ G+V N LI PFGG+K SG+GREG+K + + E+K + + Sbjct: 423 DIGRIFRVGEALEYGMVGVNTGLISNEVAPFGGIKQSGLGREGSKYGLEEYLEVKYLCL 481 Lambda K H 0.319 0.134 0.404 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: 520 Number of extensions: 23 Number of successful extensions: 3 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: 487 Length of database: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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 (21.8 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