GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas fluorescens FW300-N1B4

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171 Aldehyde dehydrogenase
           (EC 1.2.1.3)
          Length = 477

 Score =  323 bits (828), Expect = 8e-93
 Identities = 184/470 (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: 3   IGGDWVEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPRER 62

Query: 73  ANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTI 131
            N L +  DLM  + + LA+L  +  GK  A A+  ++  +  FL +    A +I G ++
Sbjct: 63  QNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGSSV 122

Query: 132 PGHQP-----DKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186
               P          + ++ +GV  AI  WNFP  +   K GPALA GCT+VLKPA +TP
Sbjct: 123 EVSMPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETP 182

Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246
            +AL LAEL   AG P GVF+VVTG+    G  LT NP+V KLTFTGST +G+Q+     
Sbjct: 183 LTALKLAELVLEAGYPAGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKIAM 242

Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306
           + + +V+LELGG +P IV  DADL  A  GA  + + N GQ C   +RLYVQ   +D  V
Sbjct: 243 ESMTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDNVV 302

Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366
             +      + +GNGL+  V  GPLI A+   +V  +I      GA +  GG+     G 
Sbjct: 303 ADIADIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESGATIACGGEQFG-PGY 361

Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426
           F +PT++VDV +   + ++E FGP+     F DEA+ + M+ND+ +GL +  ++ DLA V
Sbjct: 362 FVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDLAAV 421

Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476
            R+  +++ G V +N     +   PFGG K SG+GRE     IE Y E+K
Sbjct: 422 HRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELK 471


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: 581
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: 477
Length adjustment: 34
Effective length of query: 449
Effective length of database: 443
Effective search space:   198907
Effective search space used:   198907
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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