Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 303 bits (775), Expect = 1e-86 Identities = 163/467 (34%), Positives = 263/467 (56%), Gaps = 5/467 (1%) Query: 7 INGELVSGE-GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65 ++G + + G+ V NPA G VL + A++ A+ AA+ A+ W T K RA+ Sbjct: 26 VDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPAWRALTAKERAK 85 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 L D++ N + A + + GKPL A E+ +FA + + G + Sbjct: 86 TLRTWFDLMMANQEDIARIMTAEQGKPLAEA-RGEVAYAASFIEWFAEEGKRVYGDTIPQ 144 Query: 126 YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185 +L G ++ ++P+GV A+I PWN+P M K PALAAG +V+KP+ TPLTAL +A Sbjct: 145 HLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATATPLTALAMA 204 Query: 186 ELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 LA+ PAG+++++ G + +G +TG+P VR ++ TGS G+ +++ A ++K+ Sbjct: 205 VLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELMAQCAGTVKKVS 264 Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304 +ELGG AP +VF+DAD++ V+G Y N GQ C A R+ Q G+YD KL AV Sbjct: 265 LELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVYDAFAAKLAEAV 324 Query: 305 ATLKSG-APDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPT 363 LK G E + GPL +A +E+V + +A G +V+ GG++ + G ++ PT Sbjct: 325 KALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKG-ARVVLGGKRHELGGSFFEPT 383 Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423 +LA + ++E FGPV + F+ EE+ V AN +++GLA+ +++D+GR RV+ Sbjct: 384 ILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSRDIGRVWRVAE 443 Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 L+YG +N + P GG K SG G++ S YG+EDY ++++ Sbjct: 444 ALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIKYL 490 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: 522 Number of extensions: 19 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: 497 Length adjustment: 34 Effective length of query: 440 Effective length of database: 463 Effective search space: 203720 Effective search space used: 203720 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