Align aldehyde dehydrogenase-like protein yneI (characterized)
to candidate PfGW456L13_3880 Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
Query= CharProtDB::CH_024181 (462 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3880 Length = 463 Score = 612 bits (1578), Expect = e-180 Identities = 305/459 (66%), Positives = 360/459 (78%) Query: 3 ITPATHAISINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGK 62 ++ THAISINPATGEQ+ P+ ++ AL AA GFR WR ++ RA+ L ++G+ Sbjct: 4 VSSLTHAISINPATGEQIGHYPFESDSALQAALTRAATGFRAWRGKPVEQRAQLLINLGQ 63 Query: 63 ALRARSEEMAQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLKAEPTLVENQQAVI 122 ALR ++ MA MIT+EMGKPI QAR E+ K A LC WYAEHGPAML EPTLVE +A I Sbjct: 64 ALRNNAQAMANMITQEMGKPIAQARGEIEKCAQLCQWYAEHGPAMLSPEPTLVEGGKARI 123 Query: 123 EYRPLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIP 182 EYRPLG ILA+MPWNFP+WQV+RGAVP +LAGN Y+LKHAPNVMG L+ + FK A P Sbjct: 124 EYRPLGPILAVMPWNFPIWQVLRGAVPTLLAGNTYVLKHAPNVMGSTYLLLEAFKQADFP 183 Query: 183 QGVYGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFI 242 +GV+ +N DGVS+ I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSDPFI Sbjct: 184 EGVFEVINVTPDGVSKAIADPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSDPFI 243 Query: 243 VLNDADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRD 302 VL+DADL+ AVKAAV GRYQNTGQVCAAAKR I+E+GIA FT +FV A L +GDP Sbjct: 244 VLDDADLDEAVKAAVIGRYQNTGQVCAAAKRLIVEQGIAREFTRKFVEATQQLVVGDPLA 303 Query: 303 EENALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAF 362 +GPMARFDLRDEL QV TL +GA LL+GG+K G GNYY PTVL +VT +MT+F Sbjct: 304 TTTYIGPMARFDLRDELDQQVRDTLKEGATLLMGGKKAEGPGNYYEPTVLGDVTDQMTSF 363 Query: 363 REEMFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGY 422 ++E+FGPVA+I A+DA HALELANDSEFGL+AT++T + A+QMA+ LE GGVFINGY Sbjct: 364 KQELFGPVASIITARDAAHALELANDSEFGLTATLYTRNVELAQQMASELETGGVFINGY 423 Query: 423 CASDARVAFGGVKKSGFGRELSHFGLHEFCNIQTVWKDR 461 ASD RV+FGGVKKSGFGRELSHFG+ EFCN QTVW DR Sbjct: 424 SASDPRVSFGGVKKSGFGRELSHFGVREFCNAQTVWLDR 462 Lambda K H 0.319 0.134 0.397 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: 589 Number of extensions: 14 Number of successful extensions: 1 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: 462 Length of database: 463 Length adjustment: 33 Effective length of query: 429 Effective length of database: 430 Effective search space: 184470 Effective search space used: 184470 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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