Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Cola:Echvi_0535 Length = 514 Score = 258 bits (659), Expect = 3e-73 Identities = 158/467 (33%), Positives = 250/467 (53%), Gaps = 18/467 (3%) Query: 14 INGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAERG 73 I GEW+ S S P D ++ G VQ +T E E+ + A +A AWRK+ +RG Sbjct: 32 IKGEWLSSYS--------PVDGKEL-GKVQMTTRESYEKVLDQAEKAFKAWRKVPAPQRG 82 Query: 74 QYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGDVIPS 133 + + + + + + + EMGK+ E GE I I + G + G + S Sbjct: 83 EVVRQIGIELRNKKSLLGKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHS 142 Query: 134 TDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT---CA 190 M+ PLG+VGVIS +NFPVA+ W A V G+ V KP+ +T +T C Sbjct: 143 ERPSHRMYEQWHPLGIVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQ 202 Query: 191 KIIA-CFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARG 249 I A F G P G+ +L+ G G+ VG L + V ++ TGS Q+GK +G+ R Sbjct: 203 LIAADVFNRNGFPEGITSLLIG-GANVGAFLTQDPRVALISATGSTQMGKSVGETVGGRL 261 Query: 250 AKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKL 309 K LE+GG N +I+ + ADL+ A + GA + GQ+CT+T R+I+ ++E KE++ Sbjct: 262 GKVLLELGGNNAIIITEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERM 321 Query: 310 LQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNG 369 + +TIG+ L ED +GP+ K+ + N L+ IE+ K EG ++ G LE +Y +G Sbjct: 322 VAAYSKLTIGNPLDEDNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYVSG 381 Query: 370 YYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGR 429 YV+P++F+ + I Q+E FGP++ L+K +EA+ + N+V GLS++I T N+ Sbjct: 382 CYVRPSVFE-AENHFQIVQKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMRE 440 Query: 430 MLSFI--DEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAA 474 ++ + D G+ +N ++G E+ FGG K++ RE G A Sbjct: 441 AERYLSSEGSDCGISNVNIGTSGAEIGGAFGGEKETGG-GRESGSDA 486 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: 563 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 488 Length of database: 514 Length adjustment: 34 Effective length of query: 454 Effective length of database: 480 Effective search space: 217920 Effective search space used: 217920 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