Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF4164 Psest_4237 succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__psRCH2:GFF4164 Length = 482 Score = 340 bits (872), Expect = 6e-98 Identities = 183/462 (39%), Positives = 264/462 (57%), Gaps = 1/462 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YIDG ++ I V NPAT + +P A + R+AIDAAERA P W L A ER+ Sbjct: 14 YIDGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERALPAWRDLTAKERS 73 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 LR+ + E ++ L+ E GK A+ E+A+ A +I++ AE A+R G+ I Sbjct: 74 QKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 + + I++ K+ +GVT I PWNFP +I RK PAL G T+VIKP+ TP +A+A Sbjct: 134 HQKDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALAMV 193 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 ++ + G+P+GV ++V G +G EL NPKV +S TGS G K+M A I KV Sbjct: 194 ELAERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAKLMEQCAPGIKKVS 253 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 LELGG AP IV DDADL+ AVK V S+ N+GQ C C R+YVQ G+YD F + A+ Sbjct: 254 LELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDGVYDTFAEKFQAAV 313 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369 ++ GN E +GPLI+ A +V + + AV +GAR+ GG+A G Y+ PT+ Sbjct: 314 AKLRVGNGLEEG-TDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQAHALGGSYFEPTV 372 Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429 L++V + EETFGP+ P+ F DAI+ AND+++GL S Y ++L + + Sbjct: 373 LVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYARDLGRVFRVAEA 432 Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471 L++G IN G + SG+G K+G+ +YL+ Sbjct: 433 LEYGMVGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLE 474 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: 576 Number of extensions: 18 Number of successful extensions: 2 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