Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 296 bits (759), Expect = 8e-85 Identities = 172/478 (35%), Positives = 280/478 (58%), Gaps = 11/478 (2%) Query: 14 INGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA--KTAWRKLTGAE 71 I+G+ V++ SG +P D ++ V A+DVERAV A A WR + Sbjct: 25 IDGDLVEAASGATFHNVSPRD-GQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQ 83 Query: 72 RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRKTGDV 130 + L++ A++ME+ +E+A + ++GK + +A+ + I R+YA E + K Sbjct: 84 KKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYA-EALDKVYGE 142 Query: 131 IPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCA 190 + ++ D L + PLGV+G I PWNFP+ + +WK+APAL GN+VV+KPA ++ +T Sbjct: 143 VGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202 Query: 191 KIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVG-KIIGQAALARG 249 K+ A EAGLP GV+N++ G G V G+ LA V+ + FTGS VG +++ +A + Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNL 262 Query: 250 AKYQLEMGGKNPVIV-ADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEK 308 + LE+GGK+P IV AD DLEAAA+A G F + G+ CTA SR++V++ I + F + Sbjct: 263 KRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLAR 322 Query: 309 LLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQN 368 +++ K + +GD L G + S+ Q++ L YI +GA ++GG+++ + Sbjct: 323 VIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVR--QEAG 380 Query: 369 GYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIG 428 G+YV+P IFD V + T+A+EE+FGPV+ ++ S +EA+ +AND +GL+A ++T ++ Sbjct: 381 GFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADVS 440 Query: 429 RMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFV 486 + L + AGLV +N A ++ PFGG KQ S R++ A + +K+V V Sbjct: 441 KALRGARRLKAGLVWVNGWDA-CDITMPFGGFKQ-SGFGRDRSLHALHKYADLKSVSV 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: 488 Number of extensions: 17 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 454 Effective length of database: 465 Effective search space: 211110 Effective search space used: 211110 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