Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= reanno::Caulo:CCNA_01360 (500 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 213 bits (542), Expect = 1e-59 Identities = 148/466 (31%), Positives = 232/466 (49%), Gaps = 27/466 (5%) Query: 9 IGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVA--QAAWAATNPQRR 66 I G V+ ASG P G+V V A ++ A+A A+ A W P+++ Sbjct: 25 IDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQK 84 Query: 67 ARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKG-DIQRGLEVIEFACGVPHLLKGEYT 125 V+F L+E DELA L S + GK I+D++ DI + + + GE Sbjct: 85 KAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYGEV- 143 Query: 126 QGAGPGIDV-YSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPSVPV 184 G P + Y++ +PLGV+ I P+NFP + MW PA+A GN+ +LKP+E+ P + Sbjct: 144 -GTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202 Query: 185 RLAELMIEAGLPPGVLNVVHGDKDCV-EAILDHPDIKAVSFVGSSDIAQSVFQRAGAAG- 242 +L L +EAGLPPGVLNV+ G EA+ D+ ++F GS + + + + + + Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNL 262 Query: 243 KRVQAMGGAKNHGLVMPDA-DLDQAVADIIGAAYGSAGERCMA---LPVVVPVGEKTATA 298 KRV G K+ +V D DL+ A + + GE C A L V P+ + A Sbjct: 263 KRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKD----A 318 Query: 299 LREKLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQ 358 +++ G++VG DP +G +VS YI +GA V+ G+ ++ Sbjct: 319 FLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQ--RVR 376 Query: 359 GHEEGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFT 418 GF+V PT+FD V+P +E+FGPVL ++ S +E + LA+ YG ++T Sbjct: 377 QEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWT 436 Query: 419 RNGDAAREFADQVEVGMVGIN----VPIPVPVAYHSFGGWKRSGFG 460 + A A +++ G+V +N I +P FGG+K+SGFG Sbjct: 437 ADVSKALRGARRLKAGLVWVNGWDACDITMP-----FGGFKQSGFG 477 Lambda K H 0.320 0.137 0.409 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: 609 Number of extensions: 29 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: 500 Length of database: 499 Length adjustment: 34 Effective length of query: 466 Effective length of database: 465 Effective search space: 216690 Effective search space used: 216690 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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