Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__PV4:5208453 Length = 496 Score = 222 bits (566), Expect = 2e-62 Identities = 153/483 (31%), Positives = 244/483 (50%), Gaps = 15/483 (3%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 +IN + H S ++ P+TGE V+ +VD A++ A+ A PW M Sbjct: 7 YINGQ-HTQPSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAH---GPWSEMTPL 62 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 +R R+L + L+E + LAA+ T ++GK + ++ L+ + + G G+ Sbjct: 63 NRARILFKFKALVEANMDELAAMITREHGK-VLDDAKGEIIRGLEVVEFACGIPHLLKGE 121 Query: 160 -TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218 T + G ++T ++ +GV I P+NFP+++ W A+A GN +MK +E+ P + Sbjct: 122 HTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTFIMKPSEKDPTSV 181 Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278 + +A L+ EAG P GV N+V G A + +H+D+ V+F GST I I A + Sbjct: 182 MRMAELLTEAGLPDGVFNVVNG-DKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTAAAHG 240 Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 KRV G K+ ++M DAD+D AV A + + G+ C A S ++ D VE+ Sbjct: 241 -KRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGEVGDALVEK 299 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAA----DR 394 + + ++ VGN + + E GP + K+ Y++TG EGA LL G ++ Sbjct: 300 LLPQIQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQ 359 Query: 395 GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLD 454 GYF+ +F V MTI KEEIFGPV+ I++ K E + N +G A+FT+ + Sbjct: 360 GYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHEFGNGTAIFTQSGE 419 Query: 455 KANYLSQALQAGTVWVNC-YDVFGAQSPFGGYKMS--GSGRELGEYGLQAYTEVKTVTVK 511 A + +Q G V VN V A FGG+K S G G G++ YT+ K +T + Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479 Query: 512 VPQ 514 P+ Sbjct: 480 WPK 482 Lambda K H 0.319 0.136 0.409 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: 585 Number of extensions: 27 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: 517 Length of database: 496 Length adjustment: 34 Effective length of query: 483 Effective length of database: 462 Effective search space: 223146 Effective search space used: 223146 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