GapMind for catabolism of small carbon sources

 

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

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf1N1B4_3444 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= BRENDA::P76217
         (492 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3444 Succinylglutamic
           semialdehyde dehydrogenase (EC 1.2.1.71)
          Length = 488

 Score =  592 bits (1526), Expect = e-173
 Identities = 295/483 (61%), Positives = 367/483 (75%)

Query: 2   TLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAER 61
           +L+I G+W+ GQG S    NPV+ +VLW G  A   QVE A +AAR AFP WAR +  ER
Sbjct: 3   SLYIAGEWLAGQGESFQSVNPVTQQVLWAGEGATTGQVESAVQAARQAFPGWARRTLEER 62

Query: 62  HAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRS 121
             V+E FAA L+++  EL   I  ETGKP WEAATEVT+M+NKIAIS+++Y  RTGE+  
Sbjct: 63  IGVLEAFAAALKNHADELARTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEKSG 122

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

Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241
           + W +AGLP GVLNL+QG RETG AL+A   +DGL FTGS+ TG  LH+Q SG+P+KILA
Sbjct: 183 KCWIEAGLPAGVLNLLQGARETGIALAANPGIDGLFFTGSSRTGNHLHKQFSGRPDKILA 242

Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301
           LEMGGNNPL++D+VAD+DAAV+  IQSAF++AGQRCTCARRLL+  GA GD  LARLVAV
Sbjct: 243 LEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDTLLARLVAV 302

Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPG 361
           S  +  G +D +P PF+G +IS  AA+ ++ A + L A G   LL     QA  +LLTPG
Sbjct: 303 SSTIEVGAFDQQPAPFMGSVISLGAAKALMDAQEHLLANGAVALLEMTQPQAQAALLTPG 362

Query: 362 IIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLE 421
           I+++T VA  PDEE+FGPLL+V RY  F+ AI  AN+T +GL+ GL+S    ++ Q  LE
Sbjct: 363 ILDVTAVADRPDEELFGPLLQVIRYADFEAAIAEANDTDYGLAAGLLSDSEARYQQFWLE 422

Query: 422 ARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLN 481
           +RAGIVNWNK LTGAAS+APFGG+GASGNHR SA+YAADYCA+P+ASLE+ SL LPATL 
Sbjct: 423 SRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAADYCAYPVASLETPSLVLPATLT 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: 803
Number of extensions: 36
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: 488
Length adjustment: 34
Effective length of query: 458
Effective length of database: 454
Effective search space:   207932
Effective search space used:   207932
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 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