Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate RR42_RS25010 RR42_RS25010 betaine-aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Cup4G11:RR42_RS25010 Length = 485 Score = 320 bits (819), Expect = 9e-92 Identities = 183/475 (38%), Positives = 279/475 (58%), Gaps = 9/475 (1%) Query: 4 KLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF--AEWGQTTP 60 +LLI G V + G+ V NP+T ++L +AEA++ +DAAV AA AF + W +P Sbjct: 14 RLLIGGRWVEAASGKTFEVINPSTEELLCHVAEANSADIDAAVAAARHAFDNSSWVGMSP 73 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 R LL++AD I+ + A +E+ + G PL + A D+FR++ G + G Sbjct: 74 HARTRALLRIADQIDRHADELAAIETLDNGMPLWFSTAVATTA-ADIFRYYGGWCTKILG 132 Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 G +R +PLGV I PWN P++MA+ KLA AL GN ++LKP+E+ LT Sbjct: 133 STIPSDASGFVYTLR-EPLGVCGQIIPWNVPILMASIKLANALCCGNTLILKPAELACLT 191 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASS 239 +L+LAEL ++ P GVIN+L G G T G L HP V ++ TGS A G+ I+ + S+ Sbjct: 192 SLRLAELIQETDLPPGVINMLPGFGATAGAALALHPDVDKIAFTGSTAIGKQIVQASTSN 251 Query: 240 IKRTHMELGGKAPVIVFDDADIEAVVEG-VRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 +K+ +ELGGK+P ++F DAD++ V+ V+TF N+GQ C+A R++ + ++D + E Sbjct: 252 LKKVTLELGGKSPNVIFADADLDKAVQAAVKTF-CGNSGQVCSAGTRLFVHESVHDEVSE 310 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY 358 ++ AT G P T+LGPL S +RV +E +A G + GG + G GY Sbjct: 311 RVTRLAATYTVGDPLAPDTKLGPLISAKQRDRVLSYIEAGQAGG-ASLQLGGSQWSGRGY 369 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 + AP + G I Q+E+FGPV+S+ PF +E+ V ND+ YGL+++VWT+DV RA Sbjct: 370 FVAPAVFDGVTNGMRIAQEEIFGPVLSIIPFRDEDDAVFKGNDTTYGLSAAVWTRDVARA 429 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 H+V+ L+ G W+NT+ MP GG K SG+G++ ++ YT V+ VM++ Sbjct: 430 HKVARALKAGRVWINTYGEADPAMPFGGYKQSGWGREFGQESIDAYTQVKAVMLR 484 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: 552 Number of extensions: 26 Number of successful extensions: 5 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: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 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