Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_009562902.1 RSPH17029_RS04350 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000015985.1:WP_009562902.1 Length = 483 Score = 317 bits (811), Expect = 8e-91 Identities = 177/469 (37%), Positives = 271/469 (57%), Gaps = 4/469 (0%) Query: 14 YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 +VDG ++ + G I V PATGE I + + A A+ + +A AW A+ ERA Sbjct: 10 FVDGRPLEDETGAPIPVIYPATGEEIARLHEATPAVIEAALASGARAQAAWAAMRPVERA 69 Query: 74 NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAK-GEIAYAASFLEWFGEEAKRIYGDTIP 132 LRR DL+ ++L+ L T++ GKPL E + A A LE+F A + G+T+P Sbjct: 70 RILRRASDLIRARNEELSLLETLDTGKPLQETLVADWASGADALEFFAGLAPAVTGETVP 129 Query: 133 GHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192 Q + I++P+G+ I WN+PS + KA PALA G MV KP+ TP AL L Sbjct: 130 LGQDF--VYTIREPLGLCVGIGAWNYPSQIACWKAAPALALGNAMVFKPSEVTPLGALKL 187 Query: 193 AELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252 AE+ AG+P G+F+VV G G VG L ++ V K++ TGS GR++ A A+ ++ V Sbjct: 188 AEILIEAGLPPGLFNVVQGR-GAVGAALVTDSRVAKVSLTGSVPTGRRVYAAAAEGVRHV 246 Query: 253 SLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312 ++ELGG +P IVFDDADL++A+ A++ + + GQ C R++VQ G+ +AF+ +L Sbjct: 247 TMELGGKSPLIVFDDADLESAIGAAMLGNFYSAGQICSNGTRVFVQKGIKEAFLARLAER 306 Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTI 372 + +G+ L+ V GPL+ + KV +I A ++G ++V GG+ G + +PT+ Sbjct: 307 ADAIRMGDPLDPEVQMGPLVSQAQLEKVLAYIEKARAEGGRLVCGGEASVSPGCYVQPTV 366 Query: 373 LVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQ 432 DV ++++E FGP+ V F+ E E IA +N T+FGLA+ + DL R RV Q Sbjct: 367 FADVTDAMTLAREEVFGPVMAVLDFETEEEAIARANATDFGLAAGVFTADLTRAHRVVAQ 426 Query: 433 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481 L+ G IN ++ APFGG+K SG+GRE + +E Y ++K + +G Sbjct: 427 LQAGTCWINAYNLTPVEAPFGGVKLSGVGRENGRAAVEHYTQVKSVYVG 475 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: 579 Number of extensions: 23 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 Apr 10 2024. 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