Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate PP_1481 PP_1481 medium chain aldehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Putida:PP_1481 Length = 474 Score = 322 bits (825), Expect = 2e-92 Identities = 182/471 (38%), Positives = 272/471 (57%), Gaps = 4/471 (0%) Query: 12 QAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKE 71 Q ++G V A G V NPA G + + + A+ A+ AAD+A +W + KE Sbjct: 4 QMLINGQLV-AGQGPAWTVLNPALGTALAQINEATEAQVDSAVRAADQAFDSWSQTSPKE 62 Query: 72 RANKLRRWFDLMIENQDDLARLMTIEQGKPLAEA-KGEIAYAASFLEWFGEEAKRIYGDT 130 R+ L D + + D+LARL + GKPL+ A EI A +F A+ + G Sbjct: 63 RSQALLALADAIEAHGDELARLESQNCGKPLSAALNDEIPAIADVFRFFAGAARCLGGSA 122 Query: 131 IPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSAL 190 + P ++ + P+GV A+I PWN+P M+ K PALAAG T+V+KP+ TP +AL Sbjct: 123 AGEYLPGHTSMIRRDPLGVVASIAPWNYPLMMLAWKIAPALAAGNTVVIKPSELTPLTAL 182 Query: 191 ALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIK 250 L ELA+ +P GV +++ G VG L ++P VR ++ TGS G +++ A +K Sbjct: 183 RLGELAQDL-LPPGVLNILFGRGQTVGNPLITHPKVRMVSLTGSIPTGAHIISATADSVK 241 Query: 251 KVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLK 310 ++ +ELGG AP +VFDDAD+DAA++G + N GQ C A RLYVQDG+Y+ FV++L Sbjct: 242 RMHMELGGKAPVLVFDDADIDAAIDGIRTFGFYNAGQDCTAACRLYVQDGIYERFVERLG 301 Query: 311 AAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSK-GAKVVSGGKPHALGGTFFE 369 AVA L G GPLI A+ KV + A+++ ++V+GGKP A G FFE Sbjct: 302 KAVASLKPGLQESEETELGPLISAQHRDKVAGLVQRAIAQPHIRLVTGGKPIAGDGFFFE 361 Query: 370 PTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRV 429 PT+L D ++ + ++E FGP+ V RF DEA+ + +ND+ +GLAS + RD R R+ Sbjct: 362 PTVLADALQDDEIVRNEVFGPVVSVTRFTDEAQALEWANDSNYGLASSVWTRDTGRAHRL 421 Query: 430 AEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 A +L+YG +NT + P GG K SG G++ S YG+EDY ++++ + Sbjct: 422 AARLQYGCTWVNTHFMLVSEMPHGGQKHSGYGKDMSMYGLEDYTCVRHVMI 472 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: 559 Number of extensions: 24 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: 474 Length adjustment: 34 Effective length of query: 449 Effective length of database: 440 Effective search space: 197560 Effective search space used: 197560 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