Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 315 bits (806), Expect = 3e-90 Identities = 171/469 (36%), Positives = 276/469 (58%), Gaps = 4/469 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YIDG++ G+ DVVNPA++ VI+++ D +D ++AI AA+RA PEW A ERA Sbjct: 15 YIDGRWTV--GEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANERA 72 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + +RK + E ++ L+ E GK A+ E+A+ A +ID+ AE +R G+ I + Sbjct: 73 ALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGDTIPA 132 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 + IL+ K+ +GV I PWNFP +IARK A AL G T V +PS TP +A+A A Sbjct: 133 PANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAMA 192 Query: 190 KIVDEIGLPRGVFNLVLGRGET-VGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 ++ + G+P GVFN+V+G +G+ L +P VA + TGS + G+ ++A A ++ KV Sbjct: 193 ELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKKV 252 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 +ELGG AP IV DDAD++ AV+ + S+ N+GQ C C R++VQKG+ F + A Sbjct: 253 SMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFTEKFTAA 312 Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368 + ++ G+ + + +GP+I+ A++ V + V V GA++ GG+ E + P Sbjct: 313 VANLKLGD-GLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGESFLAPV 371 Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428 ++ DV EM + E FGPV P+++FD+ +A++MAND++YGL + Y +++ + + Sbjct: 372 IVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGRIFRVAE 431 Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 GL++G +N G ++SG G K+GL +YL+ + + L Sbjct: 432 GLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCL 480 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: 547 Number of extensions: 24 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: 485 Length adjustment: 34 Effective length of query: 445 Effective length of database: 451 Effective search space: 200695 Effective search space used: 200695 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