Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate HSERO_RS07235 HSERO_RS07235 aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__HerbieS:HSERO_RS07235 Length = 477 Score = 399 bits (1026), Expect = e-116 Identities = 213/473 (45%), Positives = 297/473 (62%), Gaps = 7/473 (1%) Query: 4 KDAQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPA 63 KD QLF INGEW + +G+TI V NPAT EVIG + A+ RA+EAA K Sbjct: 3 KDVQLF-----INGEWTASASGRTIDVINPATEEVIGKIAHADRADLDRALEAASKGFET 57 Query: 64 WRALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEA 123 WR ++A ERS +RR +L+ E +++ARLMT EQGKPLAEAK E AA I+WFAEEA Sbjct: 58 WRNMSAFERSKIMRRAADLLRERAEEVARLMTMEQGKPLAEAKMETLGAADTIDWFAEEA 117 Query: 124 KRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPAS 183 +R YG +P P +VIK+P+G AA TPWNFP + RK ALAAGC++++K Sbjct: 118 RRTYGRLVPARVPGAYQMVIKEPVGPVAAFTPWNFPLNQVVRKLSAALAAGCSIIVKAPE 177 Query: 184 QTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLME 243 +TP S L+ AG+PAGV+++V G E+ L + +++K+SFTGST +G+QL Sbjct: 178 ETPASPAELIRAYADAGVPAGVINLVYGVPAEISEYLIPHPVIKKISFTGSTPVGKQLAA 237 Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303 + +K+ ++ELGG+AP +VFDDAD+D A + +K+RN GQ CV R VQ GV++ Sbjct: 238 LAGQHMKRATMELGGHAPAMVFDDADVDVAAKMLATAKFRNAGQVCVSPTRFLVQKGVFN 297 Query: 304 AFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI-- 361 AF +K +LK+GNGLE G T GP+ + + + ++ I+DAVS+GA++ +GGK I Sbjct: 298 AFVDKFVTYAEQLKVGNGLEAGITMGPVANKRRIPALEALIDDAVSQGAQLRTGGKRIGN 357 Query: 362 EGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDM 421 +G FF+PT+L ++P A EE FGPLA + F+ EVI +N +GLA+Y +A+ Sbjct: 358 KGYFFQPTVLTNLPLQARAMNEEPFGPLALINSFETLDEVITEANRLPYGLAAYAFAKSA 417 Query: 422 SRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 +A +E GM+ IN ++ PFGGIK SG G EG IE Y+ K Sbjct: 418 HTKHALAARVESGMLTINHLGLALPELPFGGIKDSGYGSEGGTEAIEAYINTK 470 Lambda K H 0.317 0.134 0.384 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: 562 Number of extensions: 23 Number of successful extensions: 2 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: 480 Length of database: 477 Length adjustment: 34 Effective length of query: 446 Effective length of database: 443 Effective search space: 197578 Effective search space used: 197578 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 (21.6 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