GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pseudomonas putida KT2440

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_4478 PP_4478 N-succinylglutamate 5-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Putida:PP_4478
          Length = 487

 Score =  591 bits (1523), Expect = e-173
 Identities = 294/483 (60%), Positives = 366/483 (75%)

Query: 2   TLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAER 61
           T +I G+W  GQG +    NPV+  V+WQG  ADA+QV+ A +AAR AFP WA+LS   R
Sbjct: 3   THYIAGNWQAGQGETLQSLNPVTQAVIWQGQGADASQVDAAVQAARQAFPAWAQLSLEAR 62

Query: 62  HAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRS 121
             V+E+FAA L+ +   +   I  ETGKP WE+ATEVT+MINK+AIS+++Y  RTGE+  
Sbjct: 63  IDVLEKFAAQLKVHAEAMAQCIGEETGKPLWESATEVTSMINKVAISVQSYRERTGEKSG 122

Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181
            + D  A LRH+PHGV+AVFGPYNFPGHLPNGHIVPALLAGN ++FKPSELTP   E  +
Sbjct: 123 PLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTV 182

Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241
             W  AGLP GVLNLVQG RETG AL+A   +DGL FTGS+ TG  LH+Q +G+P+KILA
Sbjct: 183 NCWIAAGLPAGVLNLVQGARETGVALAANPGIDGLFFTGSSRTGNLLHQQFAGRPDKILA 242

Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301
           LEMGGNNPL++DEV D+DAAV+  IQSAF++AGQRCTCARRLL+  GA GDA +ARLV V
Sbjct: 243 LEMGGNNPLVVDEVKDLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALIARLVEV 302

Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPG 361
            + +T G +D++P PF+G +IS QAA+ ++ A  +L A GG  LL     QA  +LLTPG
Sbjct: 303 CKTITVGAFDEQPAPFMGSVISLQAARALLAAQVELAAKGGVKLLEMTQPQADAALLTPG 362

Query: 362 IIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLE 421
           I+++T VA  PDEE FGPLL+V RY  FD AI  ANNT++GL+ GL+S  R ++    L 
Sbjct: 363 IVDVTAVADRPDEEFFGPLLQVIRYADFDAAIDEANNTQYGLAAGLLSDSRARYQYFWLR 422

Query: 422 ARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLN 481
           +RAGIVNWNK LTGAAS+APFGG+GASGNHR SA+YAADYCA+P+ASLE+ SL LPATL 
Sbjct: 423 SRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETASLALPATLT 482

Query: 482 PGL 484
           PG+
Sbjct: 483 PGV 485


Lambda     K      H
   0.318    0.134    0.412 

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: 781
Number of extensions: 29
Number of successful extensions: 1
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: 492
Length of database: 487
Length adjustment: 34
Effective length of query: 458
Effective length of database: 453
Effective search space:   207474
Effective search space used:   207474
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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