Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BWI76_RS13425 BWI76_RS13425 1-pyrroline dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Koxy:BWI76_RS13425 Length = 475 Score = 793 bits (2048), Expect = 0.0 Identities = 384/474 (81%), Positives = 426/474 (89%) Query: 1 MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60 MQ+ LLING+LV+GEGE PV+NPATG+ ++ IAEA+A QV+AAV AAD AF W QTTP Sbjct: 1 MQNNLLINGKLVAGEGEAVPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTTP 60 Query: 61 KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120 + RAECLL LA+VI+E+ Q A+LES NCGKPLH NDE+PA+ DVFRFFAGAARCL G Sbjct: 61 RSRAECLLALANVIDEHAQTLAKLESLNCGKPLHCVINDELPAVADVFRFFAGAARCLPG 120 Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 +AAGEYLEGHTSMIRRDP+GVVASIAPWNYPLMMAAWKLAPALAAGNCVV+KPSEITPLT Sbjct: 121 MAAGEYLEGHTSMIRRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLT 180 Query: 181 ALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240 ALKL ELAK+IFPAGV+N+LFGRG TVGDPLT H KVRMVSLTGSIATG HII HTASSI Sbjct: 181 ALKLGELAKEIFPAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTASSI 240 Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300 KRTHMELGGKAPVIVFDDADI+AVVEGVRTFG+YNAGQDCTAACRIYAQ GIYD LVEKL Sbjct: 241 KRTHMELGGKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIYDQLVEKL 300 Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYY 360 GAAVA+LK G P+DE+TELGPLSS AHL+RV AV+ A+A HI+VI GG K GNGYYY Sbjct: 301 GAAVASLKMGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKAPGNGYYY 360 Query: 361 APTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHR 420 PTLLAGA Q+DAIVQ+EVFGPVVS+T F +EEQ ++WANDSQYGLASSVWT+DVGRAHR Sbjct: 361 QPTLLAGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVGRAHR 420 Query: 421 VSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 +SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMS+YGLEDYT +RHVM+KH Sbjct: 421 LSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTIRHVMIKH 474 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: 777 Number of extensions: 24 Number of successful extensions: 1 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: 475 Length adjustment: 33 Effective length of query: 441 Effective length of database: 442 Effective search space: 194922 Effective search space used: 194922 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