Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 302 bits (774), Expect = 1e-86 Identities = 181/475 (38%), Positives = 264/475 (55%), Gaps = 12/475 (2%) Query: 15 VDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERAN 74 +DG + ++V PATGE+ P+ A+ A+ AA A P W A +++RA Sbjct: 10 IDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRAR 69 Query: 75 KLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTIPG 133 L+R DL+ D+ A L + + GKPL+ A+ +I A S L +F A I + Sbjct: 70 LLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYF---AAAIVPWSSES 126 Query: 134 HQPDKRII--VIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALA 191 H + I ++QP+GV A I+PWN P + T K PALAAG +V KP+ TP +A Sbjct: 127 HAMELGAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAAL 186 Query: 192 LAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKK 251 L EL+ AG P GV ++V G EVG L + V+ ++FTGST G Q+ A A KK Sbjct: 187 LGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKK 246 Query: 252 VSLELGGNAPFIVFDDADL-DAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLK 310 +SLELGG P IVF DADL DA ++ + S + N G+ C+C +RL VQ +YDAF ++ Sbjct: 247 LSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYL 306 Query: 311 AAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHAL-----GG 365 A V L +G+ EA G L+ + KV IA A ++G +V+ GG AL GG Sbjct: 307 AKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGG 366 Query: 366 TFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLAR 425 + PT++ + ++ E FGP+ + F DEA+ +A++N T +GLA+ + DL+R Sbjct: 367 WYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSR 426 Query: 426 VFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 R QL++G+V IN L+ + PFGG K SG+GREG + + E K +C+ Sbjct: 427 AHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNICI 481 Lambda K H 0.317 0.135 0.391 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: 558 Number of extensions: 28 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: 483 Length of database: 483 Length adjustment: 34 Effective length of query: 449 Effective length of database: 449 Effective search space: 201601 Effective search space used: 201601 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