Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 515 bits (1327), Expect = e-150 Identities = 257/478 (53%), Positives = 345/478 (72%), Gaps = 3/478 (0%) Query: 46 LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105 L++ S++ GRW F V +PAS + V D + + + A+ AA A W + S Sbjct: 9 LIKLSSYIDGRWTVGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSA 68 Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165 ER++L+RKW++LM++++++L +++T E GKPL EA+GEI Y A F++WF+EE +RVYGD Sbjct: 69 NERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGD 128 Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225 I A DKR LV+KQPVGV + ITPWNFP+AMI RK AALAAGCT V +P+ TP SA Sbjct: 129 TIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSA 188 Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285 LA+A+LA +AGIP GV+N++ A +G+VL P V+K +FTGSTA GKILL A Sbjct: 189 LAMAELAERAGIPAGVFNIV--VGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCA 246 Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345 SVK+VSMELGG APFIVFD A++D AV GA+ SK+RNAGQTCVC+NR VQ+G+ +F Sbjct: 247 TSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFT 306 Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGG 405 KF A+ +L++G+G +G T GP+I++ AV+ V K V+D VA GA +VTGG+ + G Sbjct: 307 EKFTAAV-ANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGE 365 Query: 406 NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQ 465 +F P ++++VT +M E FGPV P+I FD E EA+A+AN + GLA YFY++D + Sbjct: 366 SFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGR 425 Query: 466 IWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 I+RVAE LE GMVGVNEG+IS+ PFGGVKQSG GREGSKYG+D+YLE+KY+C GGL Sbjct: 426 IFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCLGGL 483 Lambda K H 0.318 0.135 0.400 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: 627 Number of extensions: 26 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: 523 Length of database: 485 Length adjustment: 34 Effective length of query: 489 Effective length of database: 451 Effective search space: 220539 Effective search space used: 220539 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