Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate RR42_RS11330 RR42_RS11330 aldehyde dehydrogenase
Query= BRENDA::Q9STS1 (503 letters) >FitnessBrowser__Cup4G11:RR42_RS11330 Length = 477 Score = 355 bits (911), Expect = e-102 Identities = 201/480 (41%), Positives = 277/480 (57%), Gaps = 14/480 (2%) Query: 7 RRQLFIGGQWTEPVLRKTLPVVNPATEDIIGYIPAATSEDVELAVEAARKAFTRNNGKDW 66 R +LFI G+W P + V++ TE ++G IP + D E A++AAR AF W Sbjct: 4 RDKLFINGKWVAPHGTGLINVIHSTTEAVMGRIPEGHARDAEDAIQAARAAFD-----SW 58 Query: 67 ARATGAVRAKYLRAIAAKVIERKSELANLEAIDCGKPLDEAAWDMDDVAGCFEYYADLAE 126 + +VRA Y+R IA + R ELA L A + G P+ A V G +A A+ Sbjct: 59 SATPPSVRAGYIRKIAEGLKARSEELAQLIAGEVGMPIKMAR--AIQVGGPVYNWAQAAK 116 Query: 127 GLDAKQKTPLSLPMDTFKGYILKEPIGVVGMITPWNYPLLMAVWKVAPSLAAGCTAILKP 186 LD + + +++EP+GVV ITPWNYPL KVAP+LAAGCT +LKP Sbjct: 117 LLDT-----FAFEEEVGNSLVVREPVGVVAAITPWNYPLNQITLKVAPALAAGCTVVLKP 171 Query: 187 SELASLTCLELADICREVGLPPGVLNILTGLGTEAGAPLASHPHVDKIVFTGSTTTGSSI 246 SE+A L LA++ GLPPGV N++TG G G LASHP VD + FTGST G + Sbjct: 172 SEVAPLNAFVLAEVIEAAGLPPGVFNLVTGYGPVVGEVLASHPEVDMVSFTGSTRAGKRV 231 Query: 247 MTSAAKLVKPVSLELGGKSPIIVFDDVDIDKAVEWTMFGCFWTNGQICSATSRLLVHERI 306 A+ VK V+LELGGKS ++ DD D+ AV+ T+ CF +GQ CSA +R+LV Sbjct: 232 SELGAQSVKRVALELGGKSASVILDDADLAAAVKGTVGACFLNSGQTCSAHTRMLVPRAR 291 Query: 307 ADEFLDKLVKWTKNIKISDPFEEGCRLGPVVSKGQYERVLKFVSNARNEGATVLCGGVR- 365 DE K + + DP E RLGP++S Q +RV ++ NEGA ++ GG Sbjct: 292 YDEVKAIARKVVEGYTVGDPLLESSRLGPLISAAQKDRVTGYIQRGINEGAELVAGGPEA 351 Query: 366 PEHLKKGYFVEPAIVSNVTTSMEIWREEVFGPALCVKTFSTEDEAIQLANDSQYGLAGAV 425 PE L KG+FV+P ++ NV + +EE+FGP L + + TE++A+++ANDS YGL G V Sbjct: 352 PEGLDKGFFVKPTVLGNVDPKATVAQEEIFGPVLSIICYDTEEDAVRIANDSIYGLGGGV 411 Query: 426 LSNDLERCDRVSKAFQAGIVWVNCSQPCFCQAPWGGTKRSGFGRELGEWGLENYLSVKQV 485 S D R RV++ + G V +N P QAP+GG K+SG GRE G++GLE +L K + Sbjct: 412 WSGDEARAIRVARRIRTGQVDIN-GGPFNMQAPFGGYKQSGNGREAGKYGLEEFLEYKSL 470 Lambda K H 0.318 0.135 0.421 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: 617 Number of extensions: 28 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: 503 Length of database: 477 Length adjustment: 34 Effective length of query: 469 Effective length of database: 443 Effective search space: 207767 Effective search space used: 207767 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