Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 295 bits (756), Expect = 2e-84 Identities = 178/474 (37%), Positives = 263/474 (55%), Gaps = 8/474 (1%) Query: 6 LINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKV 62 +I+G+LV + G +P G VL + A+ V+ AV A AAF + W P+ Sbjct: 24 VIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGPRQ 83 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122 + L +LA+++E + A LES + GKP+ A N +IP ++ R++A A + G Sbjct: 84 KKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYG-E 142 Query: 123 AGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTAL 182 G S +PLGV+ +I PWN+PL MA WK+APALA GN VVLKP+E +PLTAL Sbjct: 143 VGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTAL 202 Query: 183 KLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTA-SSI 240 KL LA + P GV+N++ G G G+ L V M++ TGS G ++ ++A S++ Sbjct: 203 KLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSNL 262 Query: 241 KRTHMELGGKAPVIVFDDA-DIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK 299 KR +ELGGK+P IVF D D+EA + +YN G+ CTAA R+ + I D + + Sbjct: 263 KRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLVEAPIKDAFLAR 322 Query: 300 LGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-GNGY 358 + +K G P D ST+ G + S + + A + G +V+ G R+ G+ Sbjct: 323 VIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLGGQRVRQEAGGF 382 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 Y PT+ D + ++EVFGPV+ V F +E++ + AND+ YGLA+ +WT DV +A Sbjct: 383 YVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTADVSKA 442 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 R + RL+ G WVN MP GG K SG+G+D SL+ L Y ++ V V Sbjct: 443 LRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADLKSVSV 496 Lambda K H 0.317 0.134 0.397 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: 505 Number of extensions: 21 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: 474 Length of database: 499 Length adjustment: 34 Effective length of query: 440 Effective length of database: 465 Effective search space: 204600 Effective search space used: 204600 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 (21.7 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