Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 314 bits (804), Expect = 5e-90 Identities = 174/464 (37%), Positives = 268/464 (57%), Gaps = 17/464 (3%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 +P G +I + A+ ++ A+ AA AA WG+T+ R+ LL++AD +E+N + A Sbjct: 40 SPVNGQNFCKIPRSDAQDIELALDAAHAAKDAWGKTSVTERSNILLRIADRVEQNLEYLA 99 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHT-SMIRRDPLGV 141 E+ GK + N ++P VD FR+FAG R G AA ++G+T S +PLGV Sbjct: 100 VAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSAAD--IDGNTVSYHFPEPLGV 157 Query: 142 VASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILF 201 V I PWN+PL+MAAWK+APALAAGNCVVLKP+E TP++ L L EL +D+ P GV+N++ Sbjct: 158 VGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPVSILVLLELIEDLLPPGVLNVVN 217 Query: 202 GRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF----- 256 G G G L ++ ++ TGS G HI+ A S+ + +ELGGK+P + F Sbjct: 218 GFGAEAGQALATSKRIAKLAFTGSTEVGFHILKCAAESLIPSTVELGGKSPNLYFADVMD 277 Query: 257 -DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDE 315 +D ++ VEG+ ++N G+ CT R+ Q+ IYD +EK+ A T+K G P D Sbjct: 278 QEDEYLDKAVEGM-LLAFFNQGEVCTCPSRVLIQESIYDRFIEKVLARAQTIKQGNPLDT 336 Query: 316 STELGPLSSLAHLERVGKAVEEAKATGHIKVITGG-----EKRKGNGYYYAPTLLAGALQ 370 +T++G +S +++ + K G +V+ GG E + GYY +PT++ G Sbjct: 337 ATQVGAQASQEQFDKILSYLAIGKDEG-AQVLLGGSLCQLEGEQSKGYYISPTIMKGH-N 394 Query: 371 DDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCT 430 I Q+E+FGPV+SVT F +E + + AND++YGL + VWT+D+ RA R+ +Q G Sbjct: 395 KMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGRV 454 Query: 431 WVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 W+N + + GG K SG G++ L Y ++++V + Sbjct: 455 WINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQNTKNLLVSY 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: 571 Number of extensions: 23 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: 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 Apr 09 2024. 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