Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_012044831.1 BBTA_RS22610 carnitine dehydratase
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_000015165.1:WP_012044831.1 Length = 492 Score = 310 bits (793), Expect = 9e-89 Identities = 188/479 (39%), Positives = 252/479 (52%), Gaps = 8/479 (1%) Query: 8 YVNGEWVTSETGETTEVTNP--ANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGP 65 ++ G+W +G+ E +P A P ++ + + DAA A + EW N Sbjct: 7 FIGGQWRQPASGDYFESFDPFLAQPWALIPRCD-ARDVDAAVAAARQALEQGEWANMHPS 65 Query: 66 ERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTK 125 +RG++LR G L+A+ D L I + GK E G+V FHYF A + G Sbjct: 66 QRGQLLRRFGDLIARDADHLARIEVQDNGKLYAEMRGQVGYIPQWFHYFGGLADKVEGAV 125 Query: 126 KGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVI 185 P+ YTR EPVGV A ITPWN P+ + WKLAPALAAG T+V+KP+ I Sbjct: 126 VPIDKPDMFTYTRHEPVGVVAAITPWNSPLLLATWKLAPALAAGCTIVIKPSEFTSASTI 185 Query: 186 EIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAGK 245 E+ R ++EAG P GVLNVVTG G+ VG ++G D ++FTG G V A K Sbjct: 186 ELMRLVEEAGFPPGVLNVVTGFGADVGEPLTSHKGVDKIAFTGGENSGRHVLRNAAQTFK 245 Query: 246 RVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAELV 305 R ELGGK+ LV A+ A V +G F TGQ+C A SR +VHE ++D F+ + V Sbjct: 246 RTTLELGGKSAQLVFPDADLDNAVKGVVSGIFAATGQTCIAGSRLLVHESIHDAFLDKFV 305 Query: 306 DRAESLDVGP--GTDHEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETGH 363 A + +G D ++GP ++ + L I +A EGA V GG + G Sbjct: 306 ALARTARMGDPMNMDTQVGPVTTQPQYRRVLSCIAMAREEGAECVMGGKPADRPECGQGW 365 Query: 364 FVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTEA 423 FVEPTVF V+ MRIAQEEVFGPV++VI+ + DE AVAND YGL+A + T+D A Sbjct: 366 FVEPTVFAGVNNAMRIAQEEVFGPVLSVIKFREDDEAYAVANDTAYGLAAGVWTNDQRRA 425 Query: 424 NRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTVYDSY 482 + AG V N + PFGGFK +S RE G + Y K V+ SY Sbjct: 426 FTAARRLRAGTVWTN-TYRAVSYMAPFGGFK--ASGIGRESGQDAIMEYLETKCVWMSY 481 Lambda K H 0.310 0.130 0.370 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: 569 Number of extensions: 26 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: 482 Length of database: 492 Length adjustment: 34 Effective length of query: 448 Effective length of database: 458 Effective search space: 205184 Effective search space used: 205184 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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