Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >FitnessBrowser__ANA3:7025959 Length = 496 Score = 279 bits (714), Expect = 1e-79 Identities = 172/467 (36%), Positives = 245/467 (52%), Gaps = 4/467 (0%) Query: 9 NYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQARH 68 +Y+NGE + + S I + G + A +V AAI A++AF WS R Sbjct: 6 HYVNGEHTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVTPLNRA 65 Query: 69 DSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLPS 128 L K + +EL L+ E GK L +A GE+ R + +F G L G++ Sbjct: 66 RVLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKGEHTEQ 125 Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWALA 188 V GV+ +ALGVV I P+NFP+ +P W A+A GN ++KP++ P +A Sbjct: 126 VGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSAVMRIA 185 Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248 E++++AG PAGVFN+V G V D L+ + +SF GS + I + +VQ Sbjct: 186 ELLTQAGLPAGVFNVVNGDKEAV-DTLLSHEDIQAVSFVGSTPIAEYIYSTASKHGKRVQ 244 Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMAERM 308 G KN +++ DADL QAV + +A+ S G+RC A S + + DK V+ + ++ Sbjct: 245 ALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQI 304 Query: 309 KSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGG--LVACDTEGYFLA 366 + +KVG+ L ++GP++S+ L + +++D G EGA LV G VA +GYFL Sbjct: 305 QQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLG 364 Query: 367 PTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANHF 426 LF + T MRI REEIFGPV +IVRV DY +ALA+ N EFG I T S + A HF Sbjct: 365 ACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGEAARHF 424 Query: 427 KRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYT 472 H Q GMV VN+P FGG K S +G G FYT Sbjct: 425 CHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYT 471 Lambda K H 0.318 0.134 0.391 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: 525 Number of extensions: 20 Number of successful extensions: 3 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: 481 Length of database: 496 Length adjustment: 34 Effective length of query: 447 Effective length of database: 462 Effective search space: 206514 Effective search space used: 206514 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 (21.7 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