Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= SwissProt::A1B4L2 (508 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 830 bits (2145), Expect = 0.0 Identities = 398/493 (80%), Positives = 442/493 (89%) Query: 16 PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75 PF+ RYDNFIGG+WVAP GRYF N++PI G +I +IARS+A DIE ALDAAHAAK W Sbjct: 14 PFKARYDNFIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAAKAGWA 73 Query: 76 ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135 TS A+R+ I+L+IADRME NL LATAETWDNGKPIRET+AAD+PLAIDHFRYFAG LR Sbjct: 74 RTSAADRSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLR 133 Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195 +QEGSIS+ID DT+AYHFHEPLGVVGQIIPWNFPLLMACWKLAPA+AAGNCVVLKPAEQT Sbjct: 134 SQEGSISEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQT 193 Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255 PA IMVWA +IGDLLP GVLNIVNGFGLEAGKPLASS RIAKIAFTGET+TGRLIMQYA+ Sbjct: 194 PASIMVWAEMIGDLLPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAA 253 Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315 +NLIPVTLELGGKSPNIFF DVAREDDD+ DKALEGFTMFALNQGEVCTCPSR L+QESI Sbjct: 254 QNLIPVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFALNQGEVCTCPSRALVQESI 313 Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375 Y+KFMERA++RV A+ QG P + TMIGAQAS EQ KIL Y+DIG+ EGA++L GG+ Sbjct: 314 YEKFMERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRK 373 Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435 L G+L+ GYY+EPT+F G+NKMRIFQEEIFGPV++VTTFK + EALEIANDT +GLGAG Sbjct: 374 ILPGQLADGYYVEPTVFEGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAG 433 Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495 VWSRDAN CYR GRGI+AGRVWTNCYHAYPAHAAFGGYKQSG+GRETHKMMLDHYQQTKN Sbjct: 434 VWSRDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTKN 493 Query: 496 MLVSYSPKKLGFF 508 MLVSYSPK LGFF Sbjct: 494 MLVSYSPKALGFF 506 Lambda K H 0.319 0.136 0.411 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: 897 Number of extensions: 27 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: 508 Length of database: 506 Length adjustment: 34 Effective length of query: 474 Effective length of database: 472 Effective search space: 223728 Effective search space used: 223728 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