Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate SMc00094 SMc00094 betaine aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Smeli:SMc00094 Length = 487 Score = 318 bits (814), Expect = 3e-91 Identities = 176/456 (38%), Positives = 265/456 (58%), Gaps = 13/456 (2%) Query: 24 PATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFAE 83 PATG+++ + A+ V+ A+ AA A EW +P R L + A+++ + + +E Sbjct: 29 PATGEIIARLHAATPGIVEKAIAAAKRAQPEWAAMSPTARGRILKRAAELMRQRNRELSE 88 Query: 84 LESRNCGKPLHSAFNDEIPAIVDVFRFFAGAA-RCLNGLAAGEY--LEGHTSMIRRDPLG 140 LE+ + GKP+ + + D F FF G A LNG +Y L G + +R PLG Sbjct: 89 LETLDTGKPIQETIVADPTSGADSFEFFGGVAPAALNG----DYIPLGGDFAYTKRVPLG 144 Query: 141 VVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVINI 199 V I WNYP +A WK APAL AGN +V KPSE TPL ALK+AE+ + P G+ N+ Sbjct: 145 VCVGIGAWNYPQQIACWKGAPALVAGNAMVFKPSENTPLGALKIAEILIEAGLPKGLFNV 204 Query: 200 LFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFDDA 259 + G + G L HP V VSLTGS+ TG+ + A+ +K MELGGK+P+IVFDDA Sbjct: 205 IQG-DRATGPLLVNHPDVAKVSLTGSVPTGKKVAGAAAAELKHVTMELGGKSPLIVFDDA 263 Query: 260 DIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDESTEL 319 D+E+ + G +Y+ GQ C+ R++ Q+ I + + +L + G P DE+T+L Sbjct: 264 DLESAIGGAMLGNFYSTGQVCSNGTRVFVQRKIKEPFLARLKERTEAIVIGDPLDEATQL 323 Query: 320 GPLSSLAHLERVGKAVEEAKATGHIKVITGG---EKRKGNGYYYAPTLLAGALQDDAIVQ 376 GP+ S A ++V + + KA G +++TGG G G Y PT+ A I + Sbjct: 324 GPMVSAAQRDKVFSYIGKGKAEG-ARLVTGGGIPNNVSGEGTYIQPTVFADVTDGMTIAR 382 Query: 377 KEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHF 436 +E+FGPV+ V FD+E +V+ AN +++GL++ V+T D+ RAHRV+ RL+ G W+NT+ Sbjct: 383 EEIFGPVMCVLDFDDEVEVIARANATEFGLSAGVFTADLTRAHRVADRLEAGTLWINTYN 442 Query: 437 MLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 + E+P GG K SG+G++ S+ L YT ++ V V Sbjct: 443 LCPVEIPFGGSKQSGFGRENSVAALNHYTELKTVYV 478 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: 579 Number of extensions: 27 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: 487 Length adjustment: 34 Effective length of query: 440 Effective length of database: 453 Effective search space: 199320 Effective search space used: 199320 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: 51 (24.3 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