Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AO353_24475 AO353_24475 aldehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24475 Length = 477 Score = 341 bits (874), Expect = 4e-98 Identities = 175/470 (37%), Positives = 267/470 (56%) Query: 14 YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 ++ G W + ++I V NPAT E IG + K A+ A AA+K W+ ++A ERA Sbjct: 7 FIGGVWRNTHPDESIPVINPATEEQIGLIAKASLADIEDAAIAAEKGFATWKQVSALERA 66 Query: 74 NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133 + + L+ E +++A ++T E GKPL EA GE+A A ++W EE +R YG IP Sbjct: 67 TIMHKAASLIRERAENIALILTTEHGKPLGEAMGEVAATADTIDWHAEEGRRAYGRVIPS 126 Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193 + +PIG PWNFP +K ALAAGC+++LK A++ P A+ L Sbjct: 127 RALGVHQFTVMEPIGPVVGFAPWNFPLIQAVKKVAGALAAGCSIILKGATEAPTCAVELV 186 Query: 194 ELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKVS 253 + AG+ G +++ G +G++ L ++P +RK+TFTGST +G++L + +K+ + Sbjct: 187 KAFADAGVSPGAVNLLFGDSGQISEHLIAHPSIRKVTFTGSTPVGKKLASLAGLHMKRST 246 Query: 254 LELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAAV 313 +ELGG+AP IV DDAD+ AV+ ++ +KYRN GQ CV R V V+D FV + Sbjct: 247 MELGGHAPVIVMDDADIATAVKISVAAKYRNAGQVCVSPTRFLVHSKVFDEFVSRFVEGA 306 Query: 314 AKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTIL 373 + +G+GL+ VT GP+ A + EE +ADAVS GAK+ +GG G FFEPT+L Sbjct: 307 RAVMVGDGLDPNVTMGPMAHAGRLKATEELVADAVSHGAKLETGGNRIGHKGYFFEPTVL 366 Query: 374 VDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQL 433 +VP A DE FGP+A + F D E I +N +GL++Y Y R L+ ++ + Sbjct: 367 TNVPVTARAMIDEPFGPIALINSFDDIDEAIKEANRLPYGLSAYAYTRSLSSANKLFNGI 426 Query: 434 EYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483 E G + IN ++ PFGG+K SG G EG ++ ++ K++ L + Sbjct: 427 ESGAISINHHSVALPEHPFGGVKDSGYGTEGGPGALDAFMTTKFVSLASV 476 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: 560 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: 483 Length of database: 477 Length adjustment: 34 Effective length of query: 449 Effective length of database: 443 Effective search space: 198907 Effective search space used: 198907 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