Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AO356_25485 AO356_25485 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25485 Length = 495 Score = 337 bits (864), Expect = 5e-97 Identities = 180/481 (37%), Positives = 282/481 (58%), Gaps = 10/481 (2%) Query: 2 QHKLLINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60 +H L I+G V + + V NPATG V+ ++++AS +DAAV ++ F +W QT P Sbjct: 17 RHALFIDGGYVESQSRQTLDVVNPATGQVIAQVSDASPSDIDAAVESSRRGFKQWSQTAP 76 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 VR LLKLAD++E N + A++E+ GK +H + E+ R++AG A +NG Sbjct: 77 AVRGHVLLKLADLLERNREELAQIETCQSGKIIHISRAFEVDQAAHFLRYYAGWATKING 136 Query: 121 LAAGEYL-----EGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSE 175 L E +T+ R+P+GVV I PWN+ M+A WKLA AL G V++KPSE Sbjct: 137 ETITPSLPSFAGERYTAFTLREPVGVVVGIVPWNFSTMIAIWKLASALVTGCSVIIKPSE 196 Query: 176 ITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHI-I 233 TPLT L++AELA + PAG +N+L G G+ VG L HP VS TGS+ TG + Sbjct: 197 FTPLTILRIAELAMEAGLPAGALNVLTGGGQ-VGKGLIEHPGTNKVSFTGSVPTGLAVGQ 255 Query: 234 SHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIY 293 + + + R +ELGGK D D E V G+ G+ ++GQ C AA R + + Sbjct: 256 AAMGAGLTRATLELGGKNAAGFLRDIDPEVAVNGIIEAGFLHSGQICAAAERFFVHRSQI 315 Query: 294 DTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR 353 +++++KL ++ L G+P DE TE GP+++ H ++ + +A+A + +I GG+ Sbjct: 316 ESIMDKLAQRLSKLTIGSPLDERTEFGPVTNRQHQHKLAEFFAKARAQNNT-IIHGGKLI 374 Query: 354 KGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTK 413 G G Y PT++ +DDA++ +E FGP+ + P+D EE+++ ND+ YGL++S+WT Sbjct: 375 DGPGCYVEPTIILANRRDDALLNEETFGPIATFFPYDTEEELLELMNDTPYGLSASLWTN 434 Query: 414 DVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 D+G+A R+ ++ G WVN H +L +P GG K SG G++ ++DYT ++ VM++ Sbjct: 435 DLGKALRMVPAIEAGTVWVNMHTLLDPAVPFGGSKSSGVGREFGSAFIDDYTELKSVMIR 494 Query: 474 H 474 + Sbjct: 495 Y 495 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: 549 Number of extensions: 25 Number of successful extensions: 6 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: 495 Length adjustment: 34 Effective length of query: 440 Effective length of database: 461 Effective search space: 202840 Effective search space used: 202840 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