Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417 Length = 490 Score = 321 bits (823), Expect = 3e-92 Identities = 174/460 (37%), Positives = 266/460 (57%), Gaps = 14/460 (3%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 NPA G+VL + A+ E V+ AV +A+ W T R+ L + D++ E A Sbjct: 28 NPANGEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAMERSRILRRAVDILRERNDELA 87 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI---RRDPL 139 LE+ + GK +I DV ++AG + G E + T+ RR+PL Sbjct: 88 ALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEG----EQIPLRTTSFVYTRREPL 143 Query: 140 GVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVIN 198 G+VA I WNYP+ +A WK APALAAGN ++ KPSE+T LT LKLAE+ + PAGV N Sbjct: 144 GIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGLPAGVFN 203 Query: 199 ILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHII-SHTASSIKRTHMELGGKAPVIVFD 257 +L G G+ VG LT HP++ +S TG TG+ ++ S + SS+K MELGGK+P+I+FD Sbjct: 204 VLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSLKDVTMELGGKSPLIIFD 263 Query: 258 DADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDEST 317 DAD++ + +Y++GQ CT R++ + K+ VA ++ G P+DE+T Sbjct: 264 DADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIVERVARIRVGNPEDENT 323 Query: 318 ELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK----GNGYYYAPTLLAGALQDDA 373 GPL S AH+E V + + K G +++ GG++ G + APT+ + Sbjct: 324 NFGPLVSFAHMESVLGYIAKGKEEG-ARLLCGGDRLTDGEFAKGAFVAPTVFTDCTDEMT 382 Query: 374 IVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN 433 IV++E+FGPV+S+ ++ EE+V+ AND+++GLA+ V TKD+ RAHRV +L+ G W+N Sbjct: 383 IVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLNRAHRVIHQLEAGICWIN 442 Query: 434 THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 ++MP GG K SG G++ + L ++T ++ V V+ Sbjct: 443 AWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVE 482 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: 556 Number of extensions: 24 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: 490 Length adjustment: 34 Effective length of query: 440 Effective length of database: 456 Effective search space: 200640 Effective search space used: 200640 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