Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase
Query= BRENDA::C0P9J6 (505 letters) >FitnessBrowser__Caulo:CCNA_00424 Length = 479 Score = 305 bits (782), Expect = 2e-87 Identities = 182/486 (37%), Positives = 264/486 (54%), Gaps = 25/486 (5%) Query: 11 QLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWAR 70 + ++DG W PA L V+NP TE G I G+ DVD AV AAR A +++ Sbjct: 6 KFYIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAFA-----SFSQ 60 Query: 71 APGAVRAKYLRAIAAKVIERKPELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEAL 130 R L I A+ +R ++AK + G P AW A A + Sbjct: 61 TSREERIDILERIIAEYQKRFEDMAKAITEEMGAP----AW--------LAQRAQAAMGI 108 Query: 131 DKRQNSPVSLPMETFK-----CHLRREPIGVVGLITPWNYPLLMATWKIAPALAAGCTAV 185 Q + L F+ + +EPIGV ITPWN+P+ K+ PA+A GCT V Sbjct: 109 GHVQTAAAVLKGYKFEEDRGTTRIVKEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMV 168 Query: 186 LKPSELASVTCLELADICKEVGLPSGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETG 245 LKPSE+A + +I G+P+GV N+V G GP GA LS HP+VD V+FTGS G Sbjct: 169 LKPSEIAPFSGYIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAG 228 Query: 246 KKIMASAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLIH 305 ++ +AAP VK V ELGGKSP ++ DD D +AV + +GQ C+A +R+L+ Sbjct: 229 IEVAKNAAPTVKRVHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVP 288 Query: 306 TKIAKKFNERMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGG 365 + A A++ V DP ++GPVVSE Q+ KI+ I +GAT++TGG Sbjct: 289 GARMDEVIAIAKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGG 347 Query: 366 V-RPAHLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLA 424 V RP L+KG++++PT+ ++T M I +EE+FGPV+ + + T DEA+ + NDT+YGLA Sbjct: 348 VGRPEGLDKGYYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLA 407 Query: 425 GAVISGDRERCQRLSEEIDAGCIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSV 484 V GD++ ++++ + AG + +N + P AP+GG K SG GRE G+ +L Sbjct: 408 AYVSGGDQDEVRKVASRLRAGQVTLNGAGPDL-MAPFGGYKMSGNGREWGDHAFGEFLET 466 Query: 485 KQVTEY 490 K + Y Sbjct: 467 KAILGY 472 Lambda K H 0.318 0.135 0.422 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: 643 Number of extensions: 30 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: 505 Length of database: 479 Length adjustment: 34 Effective length of query: 471 Effective length of database: 445 Effective search space: 209595 Effective search space used: 209595 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