Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 207 bits (526), Expect = 9e-58 Identities = 146/466 (31%), Positives = 231/466 (49%), Gaps = 27/466 (5%) Query: 8 IDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAA--QPKWAATNPQRR 65 IDG V SG + +P G+V V D+ AV A+AA +W P+++ Sbjct: 25 IDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQK 84 Query: 66 ARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKG-DIVRGLEVCEFVIGIPHLQKSEFT 124 V + +L+ + +ELA + S + GK I DA+ DI + C + L K Sbjct: 85 KAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEA--LDKVYGE 142 Query: 125 EGAGPGIDM-YSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPI 183 G P + Y++ +P+G+ I P+NFP + MW APA+A GN+ +LKP+E+ P + Sbjct: 143 VGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202 Query: 184 RLAELMIEAGLPAGILNVVNGDKG-AVDAILTHPDIAAVSFVGSTPIARYVYG-TAAMNG 241 +L L +EAGLP G+LNV+ G G A +A+ D+ ++F GS P+ R + +A N Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNL 262 Query: 242 KRAQCFGGAKNHMIIMPDA-DLDQAANALIGAGYGSAGERCMAIS---VAVPVGEETANR 297 KR G K+ I+ D DL+ AA A + + GE C A S V P+ + R Sbjct: 263 KRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLAR 322 Query: 298 LIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQ 357 +I+ + + +++G D G +V++ I + QGA+ V+ G+ +++ Sbjct: 323 VIE----VAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQ--RVR 376 Query: 358 GYENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYT 417 G ++ +FD V PD + + E+FGPVL V+ + +EA+ L YG ++T Sbjct: 377 QEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWT 436 Query: 418 RDGDAARDFASRINIGMVGVN----VPIPVPLAYHSFGGWKSSSFG 459 D A A R+ G+V VN I +P FGG+K S FG Sbjct: 437 ADVSKALRGARRLKAGLVWVNGWDACDITMP-----FGGFKQSGFG 477 Lambda K H 0.319 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: 523 Number of extensions: 25 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: 498 Length of database: 499 Length adjustment: 34 Effective length of query: 464 Effective length of database: 465 Effective search space: 215760 Effective search space used: 215760 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 (21.7 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