Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 196 bits (498), Expect = 2e-54 Identities = 142/462 (30%), Positives = 229/462 (49%), Gaps = 15/462 (3%) Query: 64 EVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDALRE 123 E + PAN E +A+V +A D E + A++ IWA + +R I+R+ D LRE Sbjct: 22 ETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTGIERARIMRRAVDLLRE 81 Query: 124 KIQLLGRLVSLEMGKILVEGIG-EVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALMEQW 182 + L L +L+ GK L E ++ DV +Y AGL+ I G +P R + + Sbjct: 82 RNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEGEQIPL-RDSSFVYTRR 140 Query: 183 NPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLEDNL 242 PLG+V I A+N+P+ + W A AL GN ++K + TSL ++ + +I + E L Sbjct: 141 EPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSALKLAEIFS---EAGL 197 Query: 243 LPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSL-LELGGNN 301 G LT GA +G + R+ +SFTG GK+V K + +ELGG + Sbjct: 198 PDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSSLKDVTMELGGKS 257 Query: 302 AIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIRVGN 361 +I EDADL A+ A ++GQ CT R+F+ + +L +IR+G+ Sbjct: 258 PLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEAKLLERVQRIRLGD 317 Query: 362 PWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDH----PGNYVEPTIVTGL 417 P +GPL + ++ + + + K G ++ GG+ + G +V PTI + Sbjct: 318 PQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEYAKGAFVAPTIFSDC 377 Query: 418 VHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSD 477 D IV +E F P+L + ++++E+EV N+ + GL++ + T DL R R + + Sbjct: 378 SDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADLARAHRII--HRLE 435 Query: 478 CGIVNVNI-PTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518 GI +N S A++ GG K +G GRE+G + Y R Sbjct: 436 AGICWINTWGESPAQM--PVGGYKQSGIGRENGIASLAHYTR 475 Lambda K H 0.319 0.137 0.417 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: 633 Number of extensions: 30 Number of successful extensions: 6 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: 539 Length of database: 490 Length adjustment: 35 Effective length of query: 504 Effective length of database: 455 Effective search space: 229320 Effective search space used: 229320 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 (21.7 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