GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas putida KT2440

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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