Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 337 bits (865), Expect = 4e-97 Identities = 192/460 (41%), Positives = 272/460 (59%), Gaps = 9/460 (1%) Query: 13 SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKVRAECLLKL 70 + +G NPATG L +A A+ VD AV AA AF W T R LL+L Sbjct: 32 AADGATFETINPATGKALARVAACGAQDVDRAVAAARKAFQSGVWSDTPRSARKATLLRL 91 Query: 71 ADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGH 130 + +IE + + A LE+ + GKP+ +IP + ++A A + A G Sbjct: 92 SHLIETHREELALLETLDMGKPIAETLQYDIPEAGRTYAWYAEAIDKIYDEIAPTG-PGV 150 Query: 131 TSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKD 190 + I R+PLGVVA++ PWNYPL+MA+WK+APALAAGN VVLKP+E +PLTAL+LAELA++ Sbjct: 151 LATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGNSVVLKPAEQSPLTALRLAELAEE 210 Query: 191 I-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTA-SSIKRTHMELG 248 PAGV N++ G G G L HP V ++ TGS ATG+ + ++ S++KR +E G Sbjct: 211 AGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGSTATGKRFMEYSGQSNLKRVWLECG 270 Query: 249 GKAPVIVFDDA-DIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATL 307 GK+P IVFDD D++ + + N G+ C A R+Y Q GIYD +EKL A A + Sbjct: 271 GKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGSRLYVQSGIYDAFMEKLEAHAARM 330 Query: 308 KSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK--GNGYYYAPTLL 365 + G P D +T +G + A L+RV V+ + G ++ GG++ G+Y PT+ Sbjct: 331 QPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEG-ARLRAGGKRAHTDSGGFYMQPTIF 389 Query: 366 AGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARL 425 Q IV++E+FGPV++VT F++EE+ + ANDS YGL S +WT ++ RAHRVS +L Sbjct: 390 ECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSPYGLGSGLWTSNLSRAHRVSRKL 449 Query: 426 QYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYT 465 Q G WVN + +P GG K SG G+D SL+ L+ YT Sbjct: 450 QAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALDKYT 489 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: 538 Number of extensions: 28 Number of successful extensions: 8 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