Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 283 bits (723), Expect = 1e-80 Identities = 176/470 (37%), Positives = 257/470 (54%), Gaps = 14/470 (2%) Query: 2 SVITEQNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAK 61 +++ + Y NFI G+WV G+ +P D + V S D+E A+ AA+ AK Sbjct: 11 AIVNFNSRYDNFIGGQWVAPVGGEYFDNRSPVD-GQVFCQVARSDERDIELALDAAHAAK 69 Query: 62 TAWRKLTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYA 120 AW K + ER L K AD +EQ LE +A T E GK + E + + RY+A Sbjct: 70 DAWGKTSVTERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFA 129 Query: 121 GEGMRKTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIK 180 G + G D + + + PLGVVG I PWNFP+ + WK+APAL GN +V+K Sbjct: 130 GCIRAQEGSAA-DIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLK 188 Query: 181 PATETAVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKI 240 PA +T V+ ++ ++ LPAGV+N+V G G+ GQ LA + + FTGS Q+G Sbjct: 189 PAEQTPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHH 247 Query: 241 IGQAALARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSR 294 I + A +E+GGK+P V+ +D L+ A E ++ AF + G+ CT SR Sbjct: 248 ILKCAAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLL-AFFNQGEVCTCPSR 306 Query: 295 VIVQSGIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASL 354 V++ IY++F +K++ R K I G+ L D +G AS+ Q D LSY+E G+ EGA + Sbjct: 307 VLIAESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEV 366 Query: 355 LIGGEKLE-NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIAND 413 LIGG + +G +G+Y++P I ++M + QEEIFGPVI++ EAL IAND Sbjct: 367 LIGGTSCQLSGDQSSGFYIEPTILKG-HNKMRVFQEEIFGPVISVTTFKDEAEALAIAND 425 Query: 414 VKFGLSASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQS 463 ++GL A ++T ++ R I AG V IN A A FGG K+S Sbjct: 426 TEYGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHA-YPAHAAFGGYKKS 474 Lambda K H 0.315 0.132 0.374 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: 562 Number of extensions: 25 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: 488 Length of database: 506 Length adjustment: 34 Effective length of query: 454 Effective length of database: 472 Effective search space: 214288 Effective search space used: 214288 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 (21.5 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