Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_092346115.1 BLU87_RS07020 aldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_900107645.1:WP_092346115.1 Length = 491 Score = 301 bits (772), Expect = 3e-86 Identities = 170/481 (35%), Positives = 271/481 (56%), Gaps = 12/481 (2%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 Y +I+G+WV + G + PAD ++ N+T +DV+ AV AA +A W+ ++ Sbjct: 9 YKLYIDGKWVDASDGKTFEAHCPAD-GKLLATCANATKQDVDDAVKAAWKAFPEWKDISP 67 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAI----LRYYAGEGMR 125 +R L K AD++++ E++A + + GK L E TA + + RY+AG Sbjct: 68 QDRSIILLKIADLIDENAEKLAMIESIDNGKPLRET---TAVDVPLASDHFRYFAGVIRA 124 Query: 126 KTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATET 185 + G + DK+ + R P+GV+G I PWNFP+ + WK+APAL GN VV+KP++ T Sbjct: 125 QEGQAV-MIDKNTMSIILREPIGVIGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPSSTT 183 Query: 186 AVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAA 245 +++ + + LP GV+N+VTG GS G + EH+G + + FTGS +VG I AA Sbjct: 184 SLSLLEFAKLLDTV-LPPGVVNVVTGKGSSTGNFVLEHEGFSKLAFTGSTEVGYNIADAA 242 Query: 246 LARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERF 305 + LE+GGK+ I +D E A E G + GQ C A SRV VQ IY++F Sbjct: 243 AKKLIPATLELGGKSANIYFEDCPWEKAIEGTQLGILLNQGQVCCAGSRVFVQESIYDKF 302 Query: 306 KEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGK 365 E + + K + + + MG + QL+ L+Y+E GKQEGA L+ GG+++ G+ Sbjct: 303 VEAMAEAFKKVKVNLPWADGTMMGAQIDEVQLNKILAYVEVGKQEGARLVTGGKRITTGE 362 Query: 366 YQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTE 425 GY+++P +F +V ++M IAQEEIFGPV+ +IK EE +N+AND +GL+ +++T+ Sbjct: 363 LGKGYFMEPTLFADVNNDMRIAQEEIFGPVVCVIKFKDEEEVINMANDSDYGLAGAVWTK 422 Query: 426 NIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVF 485 +I R L + G + +N + + PFGG K+S RE + + +T K ++ Sbjct: 423 DINRALRVARAVQTGRMWVNTYNQ-LPAHTPFGGYKKSGI-GRETHKMMLEHYTQTKNIY 480 Query: 486 V 486 + Sbjct: 481 I 481 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: 553 Number of extensions: 24 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: 488 Length of database: 491 Length adjustment: 34 Effective length of query: 454 Effective length of database: 457 Effective search space: 207478 Effective search space used: 207478 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 24 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