Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PfGW456L13_5044 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5044 Length = 481 Score = 274 bits (700), Expect = 6e-78 Identities = 169/477 (35%), Positives = 250/477 (52%), Gaps = 10/477 (2%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKED---IDYAAQTAAEAF 57 +A+ ++ NYINGEWV Y +NP+ E+ + K D + A A AF Sbjct: 1 VADTKRFDNYINGEWVAG--GDYSTNINPS--ELTDAIGDYAKADLAQVHAAIDAARAAF 56 Query: 58 KTWSKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAG 117 WS + R L + +EEL L+ E GK EA+GEV R +F AG Sbjct: 57 PAWSTSGIQARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAG 116 Query: 118 APSLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKP 177 + GD L S+ V R +GVVG I P+NFP+ +P W A+A GN +LKP Sbjct: 117 ECLRLSGDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKP 176 Query: 178 SERTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEH-PEIKAISFVGSKPVGEYV 236 ++ P L E+ +AG P GVFN+V G+ VV L H P++ ISF GS VG + Sbjct: 177 ADLVPGCAWALAEIISRAGFPAGVFNLVMGSGRVVGDALVHSPKVDGISFTGSVGVGRQI 236 Query: 237 YKKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGI 296 +VQ G KN I+L+DA+L+ V V +AF S G+RC A + V GI Sbjct: 237 AVSCVSRQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGI 296 Query: 297 ADEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGREN 356 D+F+ + E++ IK+G+ L G +GPV+ + ++ + YI+ G EGARLV G Sbjct: 297 HDQFVEAMAERMKSIKVGHALKAGTDIGPVVSQAQLEQDMKYIDIGQSEGARLVSGGGLV 356 Query: 357 VSD-DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415 D +GYF+ PT+F + M I ++EIF PV +++RV + + A+ +AN +EF A + Sbjct: 357 TCDTEGYFLAPTLFADSEASMRISQEEIFGPVANIVRVADYEAALAMANDTEFGLSAGIA 416 Query: 416 TSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472 T++ +F+ + AGM+ +NL PF G K S +G+ G+ + +FYT Sbjct: 417 TTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYT 472 Lambda K H 0.318 0.136 0.396 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: 553 Number of extensions: 32 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: 487 Length of database: 481 Length adjustment: 34 Effective length of query: 453 Effective length of database: 447 Effective search space: 202491 Effective search space used: 202491 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