Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 332 bits (850), Expect = 2e-95 Identities = 203/498 (40%), Positives = 288/498 (57%), Gaps = 24/498 (4%) Query: 11 FIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAAS 70 FI G+W P + N +P I +I + D++ A+DAA A K G W+ S Sbjct: 22 FIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAA---KAG--WARTS 76 Query: 71 GSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALA-DLDDVVACFEYYAGLAEELD 129 + R+R L IA +++E L E+ D GKP+ E LA D+ + F Y+AG L Sbjct: 77 AADRSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGC---LR 133 Query: 130 SKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSEL 189 S++ + + DT +Y EP+GVV I PWN+P LMA WK+APALAAG +LKP+E Sbjct: 134 SQEGSISEIDHDTI-AYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQ 192 Query: 190 ASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTT 249 + + E+ ++ LP GVLNIV G G EAG LAS P + KI+FTG ++TG IM Sbjct: 193 TPASIMVWAEMIGDL-LPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQY 251 Query: 250 AAQLVKPVSLELGGKSPIVVFEDVD------LDKVAE-WTVFGCFFTNGQICSATSRLIV 302 AAQ + PV+LELGGKSP + F+DV LDK E +T+F G++C+ SR +V Sbjct: 252 AAQNLIPVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFA--LNQGEVCTCPSRALV 309 Query: 303 HESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTG 362 ESI +F+++ +K + PL+ +G SE Q K+L + ++EGA +L G Sbjct: 310 QESIYEKFMERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAG 369 Query: 363 GRR---PEHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHY 419 G+R P L GY+VEPT+ + M+I++EE+FGPVLAV TF TEEEA+ +ANDT + Sbjct: 370 GQRKILPGQLADGYYVEPTVF-EGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAF 428 Query: 420 GLGSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENY 479 GLG+ V S D RC R + ++AG VW NC A +GG K+SG GRE + L++Y Sbjct: 429 GLGAGVWSRDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHY 488 Query: 480 LSVKQVTRYTSDEPWGWY 497 K + S + G++ Sbjct: 489 QQTKNMLVSYSPKALGFF 506 Lambda K H 0.317 0.134 0.402 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: 580 Number of extensions: 30 Number of successful extensions: 7 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: 503 Length of database: 506 Length adjustment: 34 Effective length of query: 469 Effective length of database: 472 Effective search space: 221368 Effective search space used: 221368 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 (21.6 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