Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate H281DRAFT_06351 H281DRAFT_06351 succinate semialdehyde dehydrogenase (EC 1.2.1.16)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Burk376:H281DRAFT_06351 Length = 491 Score = 541 bits (1395), Expect = e-158 Identities = 266/477 (55%), Positives = 342/477 (71%), Gaps = 6/477 (1%) Query: 7 QLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRA 66 +L R +I G+W+ A NG VTNPATG+ I V A+ R A +AA ALPAWR Sbjct: 9 ELIRPLNFIGGKWIAAANGARFPVTNPATGDTIVEVANSSAADARAATDAAASALPAWRG 68 Query: 67 LTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRI 126 +ER+ LRRW L++EN +DLA+LM+TEQGKPLAE++GE+AY AS++ WFA+EA RI Sbjct: 69 KLPRERAEILRRWHALIVENTEDLAKLMSTEQGKPLAESRGEVAYGASYVAWFADEATRI 128 Query: 127 YGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTP 186 YGD IP Q KR+ +K+ IG+ AAITPWNFP AMI RK PALAAGCT+V KPA TP Sbjct: 129 YGDIIPQQQRGKRMSAVKEAIGIVAAITPWNFPLAMIARKIAPALAAGCTVVAKPAEDTP 188 Query: 187 YSALALVELAHRAGIPAGVLSVVTGSAG---EVGGELTGNSLVRKLSFTGSTEIGRQLME 243 +ALAL LA AG+P GVL++++ S E + ++ VRK++FTGST +G+ L Sbjct: 189 LTALALAALAQEAGVPDGVLNMLSASRDQGIEAVADWLADARVRKITFTGSTPVGKHLAR 248 Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303 E A +KK+SLELGGNAPFIVFDDADLD AV G + +K+RN GQTCVC NR+YVQ GVY+ Sbjct: 249 ESAATLKKLSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYVQAGVYE 308 Query: 304 AFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE- 362 FA+ LA VA LK+ + GP+I+ +A+ K+ H+EDAV +GAKVL+GGK + Sbjct: 309 RFADLLAKRVAALKVAPATDPSAQIGPMINERAIDKIARHVEDAVKQGAKVLTGGKRLTE 368 Query: 363 --GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD 420 N++ PT+L D V EETFGP+APLFRF DEAE + ++NDT FGLA+YF+ +D Sbjct: 369 LGPNYYAPTVLTDANDGMLVCCEETFGPVAPLFRFSDEAEAVRLANDTPFGLAAYFFTQD 428 Query: 421 MSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477 + R+ RVA LE G++GIN G +S+EVAPFGG+K SG GREGSKYG++DYL IKYLC Sbjct: 429 VRRIDRVATRLEAGVIGINEGAVSSEVAPFGGVKESGYGREGSKYGLDDYLSIKYLC 485 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: 646 Number of extensions: 16 Number of successful extensions: 3 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: 491 Length adjustment: 34 Effective length of query: 446 Effective length of database: 457 Effective search space: 203822 Effective search space used: 203822 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: 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