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 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)
Query= SwissProt::Q9DBF1 (539 letters) >FitnessBrowser__Keio:14450 Length = 490 Score = 202 bits (513), Expect = 3e-56 Identities = 144/475 (30%), Positives = 231/475 (48%), Gaps = 25/475 (5%) Query: 53 GVYNGSWGGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNIWADIPAPKRGE 112 G Y + GR T PAN +A V+ A +D + + A++ IWA + A +R Sbjct: 13 GGYTSATSGR--TFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIWASMTAMERSR 70 Query: 113 IVRKIGDAFREKIQLLGRLVSLEMGKILVE-GIGEVQEYVDVCDYAAGLSRMIGGPTLPS 171 I+R+ D RE+ L +L +L+ GK E ++ DV +Y AGL + G +P Sbjct: 71 ILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIPALEGSQIPL 130 Query: 172 ERPGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSVAVT 231 PLG+V I A+N+P+ + W +A AL GN ++K + T L ++ + Sbjct: 131 RETSFVYTRR-EPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTALKLA 189 Query: 232 KIIAQV-LED---NLLPGAICSLVCGGADIGTTMARDERVNLLSFTGSTQVGKEV-ALMV 286 +I ++ L D N+LPG GA+ G + + +SFTG GK+V A Sbjct: 190 EIYSEAGLPDGVFNVLPGV-------GAETGQYLTEHPGIAKVSFTGGVASGKKVMANSA 242 Query: 287 QERFGKSLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNEV 346 + +ELGG + +I F+DADL L + A ++GQ CT R+F+ Sbjct: 243 ASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKAAF 302 Query: 347 VDRLRSAYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMD--- 403 ++ + +IR G+ +DP +GPL + +R + + K++G V+ GG V+ Sbjct: 303 EQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGDVLKGDG 362 Query: 404 -HPGNYVEPTIVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTK 462 G +V PT+ T + D IV +E F P++ + ++ E+EV N+ GL++ I T Sbjct: 363 FDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIVTA 422 Query: 463 DLGRIFRWLGPKGSDCGIVNVNI-PTSGAEIGGAFGGEKHTGGGRESGSDAWKQY 516 DL R R + + GI +N S AE+ GG KH+G GRE+G + Y Sbjct: 423 DLNRAHRVI--HQLEAGICWINTWGESPAEM--PVGGYKHSGIGRENGVMTLQSY 473 Lambda K H 0.319 0.137 0.421 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: 664 Number of extensions: 40 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