Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate BWI76_RS13425 BWI76_RS13425 1-pyrroline dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Koxy:BWI76_RS13425 Length = 475 Score = 295 bits (756), Expect = 2e-84 Identities = 179/477 (37%), Positives = 259/477 (54%), Gaps = 7/477 (1%) Query: 5 VQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALP 64 +Q+ + I+G+ V G+A + V NPAT I I + A A++AA++A W Sbjct: 1 MQNNLLINGKLVAGEGEA-VPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTT 59 Query: 65 AIERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYE 123 RA L ++ I E A ++ L GK + + E+ AD + A AR Sbjct: 60 PRSRAECLLALANVIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLP 119 Query: 124 GEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPN 183 G G ++ + +GV I PWN+P + A K+APAL GN +VIKPSE TP Sbjct: 120 GMAAGEYLEGHTSMIRRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPL 179 Query: 184 NAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243 A+ ++ EI P GV N++ GRG TVG L + KV MVS+TGS++ G I+ A Sbjct: 180 TALKLGELAKEI-FPAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTAS 238 Query: 244 NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303 +I + +ELGGKAP IV DDAD++ V+ + N+GQ C A R+Y Q GIYDQ V Sbjct: 239 SIKRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIYDQLVE 298 Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKV--ARAVEEGARVAFGGKAVEGK 361 +LG A+ +++ G P E +GPL + A L+RV V ARA+ +V GG G Sbjct: 299 KLGAAVASLKMG-PPEDETTELGPLSSQAHLDRVSAAVDAARALPH-IQVIAGGSKAPGN 356 Query: 362 GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLN 421 GYYY PTLL RQE +I+ E FGPV+ + +F E A+S ANDS YGL SS++T+++ Sbjct: 357 GYYYQPTLLAGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVG 416 Query: 422 VAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478 A + L++G T++N + H G + SG G +GL +Y + V ++ Sbjct: 417 RAHRLSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTIRHVMIK 473 Lambda K H 0.318 0.135 0.392 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: 524 Number of extensions: 32 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: 479 Length of database: 475 Length adjustment: 33 Effective length of query: 446 Effective length of database: 442 Effective search space: 197132 Effective search space used: 197132 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 Apr 09 2024. 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