Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= SwissProt::D4GP41 (482 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 309 bits (792), Expect = 1e-88 Identities = 192/481 (39%), Positives = 272/481 (56%), Gaps = 17/481 (3%) Query: 7 NYVNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDE--WRNTPG 64 N + G + +G VT+PA VVA S+ D A AV +A A D WR Sbjct: 24 NVIGGVSGPALSGRWLPVTDPATEM-VVAEAPDSDAADIARAVASAQRAFDSHVWRGLRP 82 Query: 65 PERGRILREAGTLLAQRKDELTEILTAEEGKARPEA-AGEVQRAIDIFHYFSSKAADLGG 123 +R ++L L+ + DEL+ + T + GK + A A +VQ + Y + A L G Sbjct: 83 ADREKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEG 142 Query: 124 TKKGAS----GPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASI 179 S GP YTR+EPVGV I PWN+P+AI WK+APALAAG TVVLKP+ Sbjct: 143 QTLDNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSED 202 Query: 180 APGVVIEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQ 239 P + +A EAG+P+GVLNVV G G++ G+ I + G +SFTGS+ VG++V Sbjct: 203 TPLTALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVVGHA 262 Query: 240 ATDAGKRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDD 299 A + R ELGGK+P +V + A+P++ A +A G F GQ CTA SR +VH +Y Sbjct: 263 AVENMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRR 322 Query: 300 FVAELVDRAESLDVGPGTD--HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGE 357 + EL A+ + +G G D + GP S++ + +++I A+AEGATLVAGG Sbjct: 323 VLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGG----ER 378 Query: 358 AVETGHFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVT 417 + G FV+PT+F D MR+ +EEVFGPV+AV D ++ +A AND YGL+AS+ T Sbjct: 379 VHDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWT 438 Query: 418 DDHTEANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKT 477 + A+R V ++AGVV VN L+ +P GG K+S T R+ G A ++ +T K+ Sbjct: 439 QSLSHAHRIVPRLQAGVVWVNAHNV-LDAGLPLGGIKQSG--TGRDLGRAAVEGFTELKS 495 Query: 478 V 478 V Sbjct: 496 V 496 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: 581 Number of extensions: 23 Number of successful extensions: 4 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: 500 Length adjustment: 34 Effective length of query: 448 Effective length of database: 466 Effective search space: 208768 Effective search space used: 208768 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 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