Align aldehyde dehydrogenase-like protein yneI (characterized)
to candidate Pf1N1B4_5616 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__pseudo1_N1B4:Pf1N1B4_5616 Length = 463 Score = 611 bits (1576), Expect = e-179 Identities = 301/459 (65%), Positives = 355/459 (77%) Query: 3 ITPATHAISINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGK 62 ++ THAISINPA GEQ+ P+ +E AL A AGF WR + R++ L + K Sbjct: 4 VSSLTHAISINPANGEQIGYYPFESESALEAALSRAVAGFSLWRSKPAEERSQSLITLAK 63 Query: 63 ALRARSEEMAQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLKAEPTLVENQQAVI 122 LR +E MA MIT EMGKP QAR E+ K A LC+WYAEHGPAML AEPT VE +A I Sbjct: 64 VLRGNAETMANMITLEMGKPTTQARGEIEKCAQLCEWYAEHGPAMLTAEPTQVEGGKARI 123 Query: 123 EYRPLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIP 182 EYRPLG ILA+MPWNFP+WQV+RGAVP ++AGN Y+LKHAPNVMGCA L+ + FK A P Sbjct: 124 EYRPLGPILAVMPWNFPIWQVLRGAVPALIAGNTYVLKHAPNVMGCAYLLREAFKQADFP 183 Query: 183 QGVYGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFI 242 +GV+ +N DGVS I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSDPFI Sbjct: 184 EGVFEVINVTPDGVSTAIADPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSDPFI 243 Query: 243 VLNDADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRD 302 VLNDADL+ AVKAAV GRYQNTGQVCAAAKR I+E+GI AFT +FV A L +GDP Sbjct: 244 VLNDADLDEAVKAAVIGRYQNTGQVCAAAKRLIVEQGIVEAFTRKFVEATRELVVGDPLA 303 Query: 303 EENALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAF 362 + +GPMARFDLRDEL QV++TL +GA LL+GG+K G+GN++ PTV A+VT MT+F Sbjct: 304 TDTYIGPMARFDLRDELDRQVQQTLEEGATLLMGGKKAEGSGNFFEPTVFADVTDRMTSF 363 Query: 363 REEMFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGY 422 ++E+FGPVA+I A+DA HALELANDSEFGL++TI+T D A ++A LE GGVFINGY Sbjct: 364 KQELFGPVASIITARDAAHALELANDSEFGLASTIYTRDVELAHKLAGELETGGVFINGY 423 Query: 423 CASDARVAFGGVKKSGFGRELSHFGLHEFCNIQTVWKDR 461 CA+D RV FGGVKKSGFGRELSHFG+ EFCN QTVW DR Sbjct: 424 CATDPRVTFGGVKKSGFGRELSHFGVREFCNAQTVWLDR 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: 607 Number of extensions: 17 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