Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__BFirm:BPHYT_RS22430 Length = 486 Score = 318 bits (816), Expect = 2e-91 Identities = 170/461 (36%), Positives = 260/461 (56%), Gaps = 1/461 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YI G++ +V NPAT I+ +P + R+AID A A P W A A +RA Sbjct: 17 YIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTANAAWPAWRATTAKQRA 76 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 LRK + E A +++ ++ E GK A+ E+ + A ++++ AE +R G+ I + Sbjct: 77 VILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRVNGDTIPT 136 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 + I++ K +GV I PWNFP +I RK+ PAL G I++KP+E TP +A+A A Sbjct: 137 PASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPLSALALA 196 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 + + G+PRGVFN+V G + +G E+ GNP V +S TGS G +MA A + KV Sbjct: 197 VLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQCAPTVKKVS 256 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 LELGG AP IV DDADL+ AV + S+ NSGQ C C R YV +YD F +L A+ Sbjct: 257 LELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVYDAFAEKLRVAV 316 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369 + ++ G E + + GPLIN AA+ +VE + A+ +GAR+ GGK ++ PT+ Sbjct: 317 EQLKVGRGTE-DGVTQGPLINDAAVLKVESHIEDALAKGARIVTGGKRHALGHGFFEPTV 375 Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429 L DV M + +ETFGP+ P+ F + E+ I +AND+++GL S Y++++ + + Sbjct: 376 LADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASYFYSRDIGRVWRVAEA 435 Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYL 470 L++G IN G ++SG+G +G+ +Y+ Sbjct: 436 LEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYV 476 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: 542 Number of extensions: 21 Number of successful extensions: 3 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: 486 Length adjustment: 34 Effective length of query: 445 Effective length of database: 452 Effective search space: 201140 Effective search space used: 201140 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