Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 278 bits (711), Expect = 3e-79 Identities = 167/473 (35%), Positives = 261/473 (55%), Gaps = 10/473 (2%) Query: 12 QAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPA--WRALTA 69 +A+++G + DA +T +P G ++ V A+ A+ A + W + Sbjct: 22 RAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSP 81 Query: 70 KERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYG 128 +R + R+ +L+ + D+LA L T++ GKP+A +K ++A AA + W GE +IY Sbjct: 82 VKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYD 141 Query: 129 DTIPGHQPDKRI-IVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPY 187 + P P I ++ ++P+GV AAI PWNFP M K GPALA G ++VLKP+ ++P Sbjct: 142 ELAP--TPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPL 199 Query: 188 SALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQ 247 +A+ +A+LA+ AG+P GV +V+ G VG L + V L FTGST+I +QLM Q Sbjct: 200 TAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQ 259 Query: 248 -DIKKVSLELGGNAPFIVFDDA-DLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAF 305 ++K+V LE GG +P IVF+DA DL AA E A + N G+ C +RL V+ GV D Sbjct: 260 SNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDEL 319 Query: 306 VDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP--HAL 363 + + + G+ L+ T G ++D + + V +I +GAK++ GG Sbjct: 320 IKLIVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGSQVLAET 379 Query: 364 GGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDL 423 GG + PT+ V ++++E FGP+ V F E +A++NDT +GLA+ + D+ Sbjct: 380 GGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDI 439 Query: 424 ARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476 ++ + A+ L GMV IN + APFGG K SG GR+ S + E Y E+K Sbjct: 440 SKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEVK 492 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: 568 Number of extensions: 23 Number of successful extensions: 6 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: 498 Length adjustment: 34 Effective length of query: 449 Effective length of database: 464 Effective search space: 208336 Effective search space used: 208336 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 09 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