Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF5142 PS417_26340 betaine-aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__WCS417:GFF5142 Length = 490 Score = 322 bits (826), Expect = 1e-92 Identities = 181/479 (37%), Positives = 274/479 (57%), Gaps = 13/479 (2%) Query: 4 KLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKV 62 KL I+G +G NPA G+VL ++ A+ E V+ AV +A+ W T Sbjct: 8 KLYIDGGYTDAGSDATFEAINPANGEVLAQVQRATKEDVERAVVSAEKGQKIWAAMTAME 67 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122 R+ L + D++ E A LE+ + GK +I DV ++AG + G Sbjct: 68 RSRILRRAVDILRERNDELAALETLDTGKAFSETKYVDIVTGADVLEYYAGLVPAIEG-- 125 Query: 123 AGEYLEGHTSMI--RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 + TS + RR+PLGVVA I WNYP+ +A WK APALAAGN ++ KPSE+T LT Sbjct: 126 -EQIPLRDTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLT 184 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHII-SHTAS 238 LKLAE+ + PAGV N+L G G+ VG LT HP++ VS TG TG+ ++ S ++S Sbjct: 185 TLKLAEIYTEAGVPAGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSS 244 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 S+K MELGGK+P+IVF+DAD++ + +Y++GQ CT R++ K + Sbjct: 245 SLKEVTMELGGKSPLIVFEDADLDRAADIAMMANFYSSGQVCTNGTRVFVPKHLQAAFEA 304 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK---- 354 K+ VA ++ G P D++T GPL S AH+E V + + K G +V+ GG++ Sbjct: 305 KIVERVARIRVGNPQDDNTNFGPLVSFAHMESVLGYIAKGKEEG-ARVLCGGDRLTDGEF 363 Query: 355 GNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKD 414 G + APT+ + IV++E+FGPV+S+ ++ EE+V+ AND+ +GLA+ + TKD Sbjct: 364 AKGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGLVTKD 423 Query: 415 VGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 + RAHRV +L+ G W+N ++MP GG K SG G++ + L ++T ++ V V+ Sbjct: 424 LNRAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVE 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: 542 Number of extensions: 26 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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