Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF3587 Psest_3654 succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__psRCH2:GFF3587 Length = 488 Score = 326 bits (835), Expect = 1e-93 Identities = 177/471 (37%), Positives = 277/471 (58%), Gaps = 4/471 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 Y++G++ A ++ NPAT +I +P+ + R+AI+AA+ AQP W AL A ERA Sbjct: 16 YLNGEWCEADSGARTEIFNPATGELIGAVPNMGRGETRRAIEAAQAAQPAWRALTAKERA 75 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + LR+ + E +++ ++ E GK A EVA+ A ++++ AE +R G++I + Sbjct: 76 ARLRRWYELMLENQEDLARIMTAEQGKPLAEARGEVAYAASFLEWFAEEGKRLYGDVIPA 135 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 + IL+ K +GVT I PWNFP +I RK PAL G +V+KP+ TP +A+A A Sbjct: 136 HAGDKRILVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLKPAPQTPFSALALA 195 Query: 190 KIVDEIGLPRGVFNLVLGRGET---VGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNIT 246 + + G+P G+ +++ T VG EL NP V +S TGS + G K+M A + Sbjct: 196 ALAERAGIPAGLLSVITADAATSREVGAELCENPIVRKLSFTGSTAVGIKLMQQCAPTLK 255 Query: 247 KVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLG 306 K+ LELGG AP IV DDADL+ AV+ + S+ N+GQ C CA R+YVQ GIYD FV++L Sbjct: 256 KLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNAGQTCVCANRIYVQDGIYDAFVDKLS 315 Query: 307 EAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYP 366 A+ ++ GN AE + GPLI+AAA+ +V++ + A+++GA + GGK G ++ Sbjct: 316 AAVARLKVGNGAEEG-VTTGPLIDAAAVAKVQRHLQDALDKGATLLAGGKPHALGGNFFE 374 Query: 367 PTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKA 426 PTL+ V EM++ EETFGP+ P+ F ++ I AND+++GL + Y ++L+ + Sbjct: 375 PTLVGGVTSEMAVAREETFGPLAPLFRFRDEDEVIRQANDTEFGLAAYFYARDLSRVFRV 434 Query: 427 IKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 + L++G IN G + SG+G K+GL EY++ + + L Sbjct: 435 AEALEYGMVGINTGVISTEVAPFGGMKASGLGREGSKYGLDEYVEIKYLCL 485 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: 543 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: 488 Length adjustment: 34 Effective length of query: 445 Effective length of database: 454 Effective search space: 202030 Effective search space used: 202030 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