Align aldehyde dehydrogenase-like protein yneI (characterized)
to candidate PP_3151 PP_3151 NAD+-dependent succinate semialdehyde dehydrogenase
Query= CharProtDB::CH_024181 (462 letters) >FitnessBrowser__Putida:PP_3151 Length = 461 Score = 610 bits (1573), Expect = e-179 Identities = 304/459 (66%), Positives = 364/459 (79%), Gaps = 2/459 (0%) Query: 3 ITPATHAISINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGK 62 I+ THAIS++P +GEQ+ P+ +E ALQ A G+R WR+ ++ R+E L + Sbjct: 4 ISSLTHAISLDPYSGEQIGTYPFDTDAALEAALQRAKVGYRQWRQVSLGQRSEYLLALAD 63 Query: 63 ALRARSEEMAQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLKAEPTLVENQQAVI 122 L A++E A MI+RE+GKPI QAR EV+K LC WYAEHGPAML AEPT VE +A I Sbjct: 64 TLEAKAEAFAHMISREIGKPIAQARGEVSKCVGLCRWYAEHGPAMLAAEPTQVE--KARI 121 Query: 123 EYRPLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIP 182 EYRPLG ILA+MPWNFP+WQV+RGAVP ILAGN Y+LKHAPNVMG A L+A++FKDAG+P Sbjct: 122 EYRPLGPILAVMPWNFPVWQVLRGAVPAILAGNTYVLKHAPNVMGSAYLMAELFKDAGLP 181 Query: 183 QGVYGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFI 242 +GV+ LN DGV++ I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSDPFI Sbjct: 182 EGVFEVLNVTPDGVTRAINDPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSDPFI 241 Query: 243 VLNDADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRD 302 VL DADL+ AV+AAV GRYQNTGQVCAAAKR I+E I AFT +FV A LK+G+P + Sbjct: 242 VLADADLDAAVQAAVIGRYQNTGQVCAAAKRLIVEASIVDAFTHKFVEATRQLKVGNPLE 301 Query: 303 EENALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAF 362 ++ +GPMAR+DLRDEL QV+ TLA+GA LLLGG K+ G N+Y PTV ANVTP+MTAF Sbjct: 302 DDTYIGPMARYDLRDELDGQVQATLAEGATLLLGGNKVEGVANFYAPTVFANVTPDMTAF 361 Query: 363 REEMFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGY 422 ++E+FGPVAAI A+DA+HA+ELANDSEFGL++TI+T D A +M A L+ GGVFINGY Sbjct: 362 KQELFGPVAAIITARDADHAVELANDSEFGLASTIYTADYALAERMTAALDTGGVFINGY 421 Query: 423 CASDARVAFGGVKKSGFGRELSHFGLHEFCNIQTVWKDR 461 CASD RVAFGGVKKSGFGRELSHFG+ EF N QTVW DR Sbjct: 422 CASDPRVAFGGVKKSGFGRELSHFGVREFTNAQTVWLDR 460 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: 578 Number of extensions: 14 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: 462 Length of database: 461 Length adjustment: 33 Effective length of query: 429 Effective length of database: 428 Effective search space: 183612 Effective search space used: 183612 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