Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_022949182.1 H035_RS0111795 aldehyde dehydrogenase family protein
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_000421465.1:WP_022949182.1 Length = 506 Score = 273 bits (697), Expect = 1e-77 Identities = 180/486 (37%), Positives = 247/486 (50%), Gaps = 17/486 (3%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 Y N+I G W+ +G + P V STAED+E+A+ AA+ AK AW K + Sbjct: 19 YNNYIGGHWIAPVNGQYFENITPVTGTPFCE-VARSTAEDIEKALDAAHAAKDAWGKTSP 77 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGD 129 A R L K AD MEQ+LE +A T + GK + E A Y +R Sbjct: 78 AGRADLLLKIADRMEQQLEMLAVAETWDNGKPIRETLAADIPLAADHFRYFASAIRTQES 137 Query: 130 VIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTC 189 + D D + + PLGVVG I PWNFP+ + WK+APAL GN VV+KPA +T Sbjct: 138 SVCEIDADTIAYHFHEPLGVVGQIIPWNFPLLMASWKLAPALAAGNCVVLKPAEQTP--- 194 Query: 190 AKIIACFEEAG--LPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALA 247 A I+ E G +P GV+N+V G G G+ LA + V FTG G++I Q A Sbjct: 195 ASILVLMELIGDLIPPGVVNVVNGFGVEAGKPLARSSRIAKVAFTGETTTGRLIMQYASQ 254 Query: 248 RGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGI 301 LE+GGK+P V D ++ A E + A + G+ CT SR ++Q+ I Sbjct: 255 NLIPVTLELGGKSPNLFFEDVTAKQDTFVDKALEGFASFAL-NQGEVCTCPSRALLQASI 313 Query: 302 YERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKL 361 Y+ F + L+R K I G+ L + +G AS Q++ LSYI+ +QEG LIGGE+ Sbjct: 314 YDDFIHRALERVKAIRQGNPLDTETMIGAQASAEQMEKILSYIDIARQEGTECLIGGERA 373 Query: 362 E-NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSA 420 + G+ GYY+QP IF ++M + QEEIFGPV+A+ EEAL IAND +GL A Sbjct: 374 QLQGELAGGYYIQPTIFKG-HNQMRVFQEEIFGPVLAVTTFRDEEEALEIANDTLYGLGA 432 Query: 421 SIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTA 480 ++T ++ I AG V N A FGG KQS RE + D + Sbjct: 433 GVWTRDMNTAYRMGRGIQAGRVWTNCYHL-YPAHAAFGGYKQSGI-GRETHKMMLDHYQQ 490 Query: 481 IKTVFV 486 K + V Sbjct: 491 TKNLLV 496 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: 571 Number of extensions: 23 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 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