Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 328 bits (840), Expect = 3e-94 Identities = 184/479 (38%), Positives = 275/479 (57%), Gaps = 9/479 (1%) Query: 2 QHKLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60 + +L I+G V + E NPA G+VL ++AEA A ++ AV +A+ W T Sbjct: 6 RQQLYIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTG 65 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 RA + + D++ E A LE+ + GKPL + +I DV ++AG A + G Sbjct: 66 IERARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEG 125 Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 + RR+PLGVVA I WNYP+ +A WK APALAAGN ++ KPSE+T L+ Sbjct: 126 EQI-PLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLS 184 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASS 239 ALKLAE+ + P GV N+L G G VG +T HP++ VS TG +ATG+ +++ ASS Sbjct: 185 ALKLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASS 244 Query: 240 -IKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 +K MELGGK+P+I+ +DAD++ + ++++GQ CT R++ G+ Sbjct: 245 SLKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEA 304 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEK----RK 354 KL V ++ G P E T GPL S AH+ V + + KA G +++ GGE+ Sbjct: 305 KLLERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAG-ARLLCGGERVTEGEY 363 Query: 355 GNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKD 414 G + APT+ + D AIV +E+FGPV+S+ + +E++V+ AND++YGLA+ V T D Sbjct: 364 AKGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTAD 423 Query: 415 VGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 + RAHR+ RL+ G W+NT ++MP GG K SG G++ + L YT V+ V V+ Sbjct: 424 LARAHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQVE 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: 560 Number of extensions: 27 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