Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate BPHYT_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS34305 Length = 479 Score = 628 bits (1619), Expect = 0.0 Identities = 299/477 (62%), Positives = 374/477 (78%), Gaps = 2/477 (0%) Query: 7 KLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRA 66 + R ++ G W + T V NPATGE++ V K GAAET +AI AA++A PAWRA Sbjct: 3 EFLRTGHFIGGEWYEG--ADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRA 60 Query: 67 LTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRI 126 LTAKER+ +++RW +LM+EN+D LA L+T+EQGKPLAEA+GE+ YAASF EWF EEAKR Sbjct: 61 LTAKERSARVKRWGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRA 120 Query: 127 YGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186 YGD IP P+ +IIV ++P+GV AAITPWNFP AMITRKAGPALAAGCTMVLKP+ +TP Sbjct: 121 YGDVIPSPNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETP 180 Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246 SA ALA LA +AGIP GVF++V+G A +GG LT + +VRKL+FTGST +G+ L + A Sbjct: 181 LSAFALAVLAAKAGIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSA 240 Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306 +KK+SLELGGNAPFIVFDDADLDAAV+GA+ SK+RN GQTCVC NR YVQDG+YDAF Sbjct: 241 DTLKKLSLELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFT 300 Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366 L AV K+ +GN L+ V GPLI+ A+ KVE H+ADA+ KGAK+++GGKPH LGGT Sbjct: 301 SALTQAVRKMRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGT 360 Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426 F+EPT+L D + L++ +ETFGP+A FRFK EAE I +NDT FGL++YFY RDLAR Sbjct: 361 FYEPTVLADADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLARA 420 Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483 +RV E LE GMVGIN G++S EVAPFGG+K SGLGREGSKYG+++Y E+KY+ +GG+ Sbjct: 421 WRVGEALESGMVGINEGIVSTEVAPFGGVKQSGLGREGSKYGLDEYTELKYMMMGGL 477 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: 676 Number of extensions: 10 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: 483 Length of database: 479 Length adjustment: 34 Effective length of query: 449 Effective length of database: 445 Effective search space: 199805 Effective search space used: 199805 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