GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens GW456-L13

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360
          Length = 496

 Score =  325 bits (834), Expect = 2e-93
 Identities = 186/470 (39%), Positives = 266/470 (56%), Gaps = 9/470 (1%)

Query: 15  VDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP--AWRALTAKER 72
           + G WV+A +GQT+ ++NPATGE++  VP+    +  RA+ AA +A    AW     +ER
Sbjct: 22  IGGDWVEAADGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPRER 81

Query: 73  ANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTI 131
            N L +  DLM  + + LA+L  +  GK  A A+  ++  A  FL +    A +I G T+
Sbjct: 82  QNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTV 141

Query: 132 PGHQP-----DKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186
               P          + ++ +GV  AI  WNFP  +   K GPALA GCT+VLKPA +TP
Sbjct: 142 DVSAPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETP 201

Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246
            +AL LAEL   AG P+GVF+VVTG+    G  LT NP+V KLTFTGST +G+Q+     
Sbjct: 202 LTALKLAELVLEAGYPEGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKIAM 261

Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306
             + +V+LELGG +P IV  DADL  A  GA  + + N GQ C   +RLYVQ   +D  V
Sbjct: 262 DSMTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDNVV 321

Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366
             +      + +GNGL+  V  GPLI A+   +V  +I      GA +  GG+     G 
Sbjct: 322 ADISDIANAMKLGNGLDPSVDMGPLISARQQERVYGYIEKGRESGATIACGGEQFG-PGF 380

Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426
           F +PT++VDV +   + ++E FGP+     F DEA+ + M+ND+ +GL +  ++ DLA V
Sbjct: 381 FVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDLAAV 440

Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476
            R+  +++ G V +N     +   PFGG K SG+GRE     IE Y E+K
Sbjct: 441 HRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELK 490


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: 588
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: 496
Length adjustment: 34
Effective length of query: 449
Effective length of database: 462
Effective search space:   207438
Effective search space used:   207438
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