Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Putida:PP_3646 Length = 493 Score = 354 bits (909), Expect = e-102 Identities = 195/474 (41%), Positives = 281/474 (59%), Gaps = 6/474 (1%) Query: 8 LFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP--AWR 65 L R Q +DG W DA +G+T NPAT + +P A+ A++AA +A AWR Sbjct: 3 LVRFQMCIDGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFDSKAWR 62 Query: 66 ALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKR 125 ++TA R LRR DL+ EN++ LA+L + + GK + E +G++ Y F + A + Sbjct: 63 SITATARGKLLRRLGDLIAENKEHLAQLESRDNGKLIRETRGQVGYLPEFFHYTAGLADK 122 Query: 126 IYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQT 185 + G T+P +PD + +PIGV A I PWN P + K PALAAG T+VLKP+ Sbjct: 123 LEGGTLPLDKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEHA 182 Query: 186 PYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAEC 245 + L LA LA AG P GV +VVTG G LT +P+VRK+ FTG R ++ Sbjct: 183 SATILELARLALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRSS 242 Query: 246 AQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAF 305 A++ K+SLELGG +P I+F DADLD+A+ GA+ Y +GQ+CV +RL VQD ++D F Sbjct: 243 AENFAKLSLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDEF 302 Query: 306 VDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHAL-- 363 V++L A ++ IGN + GP+ A+ +A VE +A A ++GAK+ GGK + Sbjct: 303 VERLIARAKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADVEG 362 Query: 364 GGTFFEPTILVDVPKNAL-VSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARD 422 G F+EPT L + NA+ + ++E FGP+A V RFK E E +AM+ND++FGLA+ + RD Sbjct: 363 DGWFYEPT-LFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAGIWTRD 421 Query: 423 LARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476 L R R+A + G++ +NT + +AP GG K SG GRE + Y E+K Sbjct: 422 LGRAHRLARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELK 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: 594 Number of extensions: 27 Number of successful extensions: 3 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: 493 Length adjustment: 34 Effective length of query: 449 Effective length of database: 459 Effective search space: 206091 Effective search space used: 206091 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 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