Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__BFirm:BPHYT_RS29875 Length = 483 Score = 348 bits (892), Expect = e-100 Identities = 186/466 (39%), Positives = 277/466 (59%), Gaps = 4/466 (0%) Query: 2 QHKLLINGE-LVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60 +H LLI+G+ L G GE NPAT + + +A+ SA VD AVRAA AA W Sbjct: 9 RHDLLIDGKRLPPGTGEYSVDINPATEEPIALVAQGSAADVDTAVRAARAALKVWNGIRT 68 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 RA L++LA ++ N + A LES + GKP+ + +IPA +D ++AG +NG Sbjct: 69 AERARILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKING 128 Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 + T +R +P+GVVA+I PWN+PLM+ WK+APALA G +++KP+EITPLT Sbjct: 129 QVVPVRPDALTYTLR-EPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLT 187 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASS 239 AL++ ELA + P GV+NI+ G+G+ VGD L HP V V+ TGS + G I+ A + Sbjct: 188 ALRIGELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAGN 247 Query: 240 IKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK 299 KR +ELGGK+ ++F DA+++ V + ++N GQ C+A RI A + +YD +VE+ Sbjct: 248 FKRVTLELGGKSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVER 307 Query: 300 LGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYY 359 L A ++K G P T +GPL S A ++ V VE +A G ++TGG + G++ Sbjct: 308 LAARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEG-ASLVTGGARVGERGFF 366 Query: 360 YAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAH 419 PT+ A + I Q+E+FGPV SV F++E + AN + Y LA+ VW+ D+GR H Sbjct: 367 VEPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVH 426 Query: 420 RVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYT 465 RV+ L+ G W+NT+ +P GG SG+G++ +E++T Sbjct: 427 RVARDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFT 472 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: 563 Number of extensions: 25 Number of successful extensions: 4 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: 483 Length adjustment: 34 Effective length of query: 440 Effective length of database: 449 Effective search space: 197560 Effective search space used: 197560 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: 51 (24.3 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