Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate RR42_RS21760 RR42_RS21760 succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Cup4G11:RR42_RS21760 Length = 482 Score = 319 bits (818), Expect = 1e-91 Identities = 171/461 (37%), Positives = 265/461 (57%), Gaps = 3/461 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YIDG++ IDV NPAT + ++P A++ R+AI+AA RA P W A A ER+ Sbjct: 15 YIDGRWTD--AQRHIDVTNPATGERVGQVPLLGADETRQAIEAANRALPAWRARTAKERS 72 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + LRK + +++ ++ E GK A E+ + A +I++ AE +R GE I + Sbjct: 73 ALLRKWFELLLANQDDLARIMTAEQGKPFAEARGEIGYAASFIEWFAEEGKRVYGETIPA 132 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 + I++ K +GV I PWNFP +I RK PAL G T+V+KP+ TP A+A Sbjct: 133 PVSNQRIVVTKEPVGVCAAITPWNFPAAMITRKAGPALAAGCTMVVKPASQTPLTALAMV 192 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 + + G+P GV ++V G +G EL+ NP V ++ TGS G +MA A I KV Sbjct: 193 ALAERAGIPAGVLSVVTGSAAAIGGELSSNPLVRKLTFTGSTEVGRTLMAQTASTIKKVS 252 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 +ELGG AP IV +DADL+ AV+ + S+ N+GQ C CA R+YV +YD F +L A+ Sbjct: 253 MELGGNAPFIVFEDADLDAAVEGAIVSKYRNAGQTCVCANRLYVHSKVYDAFAEKLVAAV 312 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369 +A++ GN E + + +GPLI+ A+ +VE+ + A+ +GARV GGK ++ PT+ Sbjct: 313 RALKVGNGME-DGVRIGPLIDGKAVTKVEEHITDAISKGARVLQGGKRHALGQSFFEPTV 371 Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429 L DV M + EETFGP+ P+ F+T ++ ++MAND+++GL S Y ++L + + Sbjct: 372 LADVTPGMLVAREETFGPLAPLFRFETEDEVVAMANDTEFGLASYFYARDLGRVWRVSER 431 Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYL 470 L++G +N G ++SG+G +G+ +YL Sbjct: 432 LEYGMVGVNTGLISNEVAPFGGVKQSGVGREGSHYGIEDYL 472 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: 559 Number of extensions: 23 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: 482 Length adjustment: 34 Effective length of query: 445 Effective length of database: 448 Effective search space: 199360 Effective search space used: 199360 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 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