Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >FitnessBrowser__Phaeo:GFF3227 Length = 802 Score = 310 bits (793), Expect = 2e-88 Identities = 189/469 (40%), Positives = 273/469 (58%), Gaps = 22/469 (4%) Query: 23 FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82 FINGE+T G+ FD +P G +L ++ +D AV+ AR + WS + Sbjct: 60 FINGEFT--APGDGFDSKNPATGEVLATLSQATQSDVDSAVDAARKAQTK--WSAAGGAA 115 Query: 83 RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEV 142 R + A L+++HA A+LETLD GKPI +S +IDVP A + + + E Sbjct: 116 RARYLYAIARLMQKHARLFAVLETLDNGKPIRESRDIDVPLAQRHFYYHAGMAQLMESE- 174 Query: 143 AATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALR 202 L RE +GV G I+PWNFPL+M WK+ PA++ GN+VVLKP+E + LTAL Sbjct: 175 ---------LPDREALGVCGQIIPWNFPLLMLAWKVAPAIAMGNTVVLKPAEYTSLTALL 225 Query: 203 IAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMK 262 A + +AG+PKGV+N++ G G VG+ + + DVD + FTGST + +++ + S K Sbjct: 226 FADICRQAGLPKGVVNIVTGDG-AVGEMI-VGADVDKIAFTGSTAVGRRIREATAGSG-K 282 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTFLPLV 322 + LE GGKSP IVF DA D+ +A E AI FNQG+VC AGSRLLV+ I + F + Sbjct: 283 ALTLELGGKSPYIVFDDA-DIDSAIEGLVDAIWFNQGQVCCAGSRLLVQEGIAERFHTKL 341 Query: 323 IEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEETGGTY 382 + + GNPLD + +VGA+VD Q+ T+ S + A ++ G A ++ G + Sbjct: 342 RVRMDKLRIGNPLDKSIDVGAIVDPVQLTTI-SEMVAANTAGRMHQA---QVAVPERGCF 397 Query: 383 VEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTKDISKAH 442 PT+ +G++ + + QEEIFGPVL F T +A+E+AN+T YGLAA +WT++++ A Sbjct: 398 YPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVELANNTRYGLAATLWTENVNLAL 457 Query: 443 LTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELK 491 A L AG VWVN + D A FGG ++SG GR+ YT+ K Sbjct: 458 DIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGGWEGLSAYTKPK 506 Score = 79.7 bits (195), Expect = 4e-19 Identities = 66/245 (26%), Positives = 108/245 (44%), Gaps = 15/245 (6%) Query: 25 NGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRK 84 +G Y+ A+ ++ G LLG + + D + AVE A + WS+ R Sbjct: 544 DGGYSKAIHSKS--------GGLLGHVGLGNRKDVRNAVE---AAAGANAWSKTTGHLRA 592 Query: 85 ATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAA 144 + L E A + +D S +V + Q L + DK + Sbjct: 593 QILYYIGENLSARVGEFA--DRIDRMTGKSQGAQ-EVEASIQRLFTAAAWADKYDGQAHG 649 Query: 145 TPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIA 204 P + L +EPVGV+GA+ PL+ + PA++ GN VVL SE PL+A Sbjct: 650 VPIRGVALAMKEPVGVIGALCADEAPLLGLVSVMAPAIAMGNRVVLAASEAYPLSATDFY 709 Query: 205 ALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRI 264 + + +P GV+N+L G + LA H++VD V++ S+ ++ + N+KR Sbjct: 710 QVLETSDLPGGVVNILTGRHAEMASPLASHLNVDA-VWSFSSSDLSAMIEEASAGNLKRT 768 Query: 265 WLEAG 269 W+ G Sbjct: 769 WVNNG 773 Lambda K H 0.316 0.132 0.389 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: 1024 Number of extensions: 53 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 497 Length of database: 802 Length adjustment: 38 Effective length of query: 459 Effective length of database: 764 Effective search space: 350676 Effective search space used: 350676 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 (21.6 bits) S2: 54 (25.4 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