GapMind for catabolism of small carbon sources

 

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

Align Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized)
to candidate PfGW456L13_3478 Altronate dehydratase (EC 4.2.1.7)

Query= SwissProt::P39829
         (523 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3478
          Length = 510

 Score =  286 bits (733), Expect = 1e-81
 Identities = 170/493 (34%), Positives = 265/493 (53%), Gaps = 21/493 (4%)

Query: 16  IKVHDTDNVAIIVNDNGLKAGTRFP-DGLELIEHIPQGHKVALLDIPANGEIIRYGEVIG 74
           I++   DNV +   +  +  GT    + L  ++ +P GHK+A   I     +++Y  VIG
Sbjct: 10  IRLDPADNVVVARVE--IPTGTAITNESLTTLQDVPLGHKIAARMIEKGQPVLKYNTVIG 67

Query: 75  YAVRAIPRGSWIDESMVVLPEAPPLHTLPLATKVPEPLPPLEGYTFEGYRNADGSVGTKN 134
           YA   +P G+W+    +   E    +   L     + LP  +  TF+G    DG V T+N
Sbjct: 68  YASEDLPPGTWMHSHNIEFGETARDYRYGLDYVPTDLLPADKRATFQGIIREDGRVATRN 127

Query: 135 LLGITTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAVVPIRT 194
            LGI    +C A V   +    + + L  +PN+DGVV   H  GCG+ +      +  RT
Sbjct: 128 YLGIFVVGNCGATVARKIANHFDEERLAAFPNIDGVVPFVHEIGCGMEMTGEPMNLLRRT 187

Query: 195 IHNISLNPNFGGEVMVIGLGCEK------LQPERLLTGTDDVQAIPVESASIVSLQDEKH 248
           I     + N  G ++ I LGCE+      ++ E+L+ G D ++++ ++            
Sbjct: 188 IGGHIKHANTAGGLL-IALGCERNNIYGFIEQEQLVLG-DMLKSLVIQDVG--------- 236

Query: 249 VGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASD 308
            G ++ V+  +++ +  L + N  QRET  A  L++GMQCGGSD FSG++ANPA+G A D
Sbjct: 237 -GVKTAVDQGIKMIQAMLPQANAVQRETVSAEHLIIGMQCGGSDGFSGLSANPALGAAVD 295

Query: 309 LLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRLLEEMEWYDNYLNMGKTDRSANPS 368
           +LVR G T + SE +E+    H LT RA   EVG++L++ ++W+  Y     T  +   S
Sbjct: 296 ILVRHGGTAILSETSEIFGVEHTLTARAATPEVGRKLIDRIDWWLEYNKGRDTQINGRVS 355

Query: 369 PGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKRGLIYAATPASDFVCGTQQVA 428
           PGN  GGLANV+EK+LG   K G + +++V       T  GL++  TP  D V  T Q+A
Sbjct: 356 PGNNAGGLANVLEKSLGGAKKGGNAPLMDVYEYAYPVTTHGLVFMDTPGYDPVSATGQIA 415

Query: 429 SGITVQVFTTGRGTPYGLMAVPVIKMATRTELANRWFDLMDINAGTIATGEETIEEVGWK 488
            G  +  FTTGRG+ +G +  P  K+A+ + + NR  D MDIN G I  G++TI+++G +
Sbjct: 416 GGANMIAFTTGRGSCFGSVPAPTFKLASNSPMFNRMSDDMDINCGQIIDGDKTIQQMGQE 475

Query: 489 LFHFILDVASGKK 501
           +F  +L  ASG K
Sbjct: 476 IFERLLTHASGDK 488


Lambda     K      H
   0.317    0.136    0.403 

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: 647
Number of extensions: 25
Number of successful extensions: 2
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: 523
Length of database: 510
Length adjustment: 35
Effective length of query: 488
Effective length of database: 475
Effective search space:   231800
Effective search space used:   231800
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