Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Dino:3607686 Length = 506 Score = 294 bits (753), Expect = 4e-84 Identities = 175/471 (37%), Positives = 256/471 (54%), Gaps = 15/471 (3%) Query: 15 EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVI 74 EG P TG+V+ +IA +SA V+ A+ AA AA WG+T+ RA +LK+AD I Sbjct: 32 EGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDAWGKTSVTERANIVLKIADRI 91 Query: 75 EENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI 134 EEN + A+ E+ + GKP+ +IP VD FR+FAG R G + E + Sbjct: 92 EENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEG-SMSEIDNDTVAYH 150 Query: 135 RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPA 194 +PLGVV I PWN+ ++MAAWKLAPA+AAGNC+VLKP+E TP + L EL D+ PA Sbjct: 151 FHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMVLVELISDLLPA 210 Query: 195 GVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVI 254 GV+NI+ G G VG L ++ ++ TGS ATG I+ ++ +ELGGK+P I Sbjct: 211 GVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAATVNLIPVTLELGGKSPNI 270 Query: 255 VF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLK 308 F DDA ++ VEG F +N G+ CT R + IY+ + + A V + Sbjct: 271 FFKDVMAEDDAFLDKAVEGFVLFA-FNQGEVCTCPSRALIHEDIYEEFIARAIARVKAIV 329 Query: 309 SGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNGYYYAPT 363 G P T +G +S +++ + G +V+TGG+ +G+Y PT Sbjct: 330 QGDPRKMETMVGAQASKEQKDKILSYFQIGVEEG-AEVLTGGKVADVSDDLKDGFYIEPT 388 Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423 +L G + Q+E+FGPVVSVT F EE+ + AND+ YGL + VW++D +R Sbjct: 389 ILKGH-NKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVWSRDQNTCYRFGR 447 Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 +Q G WVN + + GG K SG G++ L+ Y ++++V + Sbjct: 448 GVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNMLVSY 498 Lambda K H 0.317 0.134 0.397 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: 568 Number of extensions: 32 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: 474 Length of database: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 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