GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Shewanella loihica PV-4

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__PV4:5208066
          Length = 405

 Score =  191 bits (486), Expect = 3e-53
 Identities = 139/389 (35%), Positives = 206/389 (52%), Gaps = 35/389 (8%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL--DPLRAMLAKTLAA 135
           D +G EF+D  GG  +  +GH +P +V A++ Q  ++  H   ++  +P  A+  K + A
Sbjct: 37  DQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQ-GEKIWHLANVMTNEPALALATKLVEA 95

Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGALSATA 192
               K+   +F NSG E+ EAALKLA+ Y   +    K   IA   AFHG++   +S   
Sbjct: 96  TFAEKV---YFANSGAEANEAALKLARRYALDKFGAEKDQIIAFDKAFHGRTFFTVSVGG 152

Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252
           ++ +   F P      H+PF +I A+   ++      D   A++LEP+QGEGG+I   P 
Sbjct: 153 QAAYSDGFGPKPQSITHLPFNDIAALEAEVS------DKTCAIMLEPLQGEGGIIDADPE 206

Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312
           +L AVR L D+  AL+I DEVQTG+GR G+++A     V PDIL  AKALGGG  PI A 
Sbjct: 207 FLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVTPDILTTAKALGGG-FPIAAM 265

Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372
           + T E+ S L      H +T+GGNPLACA   A ++V+    +    +++  +L DG  Q
Sbjct: 266 LTTTEIASHL--KIGTHGSTYGGNPLACAIGNAVLDVVNTPEVLDGVKRREQLLRDGLNQ 323

Query: 373 LAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGT-------LNNAKTI 425
           +  +Y  +  E RG+G+L+    V NE  Y   S+ F    LVAGT       +     I
Sbjct: 324 INEKY-HVFTEVRGQGLLLGA--VLNE-QYQGRSKDF----LVAGTSEGLMCLIAGPNVI 375

Query: 426 RIEPPLTLTIEQCELVIKAARKALAAMRV 454
           R  P  +L I + ++    AR   A  +V
Sbjct: 376 RFTP--SLVIPEADIAEGLARFERAVAKV 402


Lambda     K      H
   0.320    0.135    0.393 

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: 369
Number of extensions: 15
Number of successful extensions: 5
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: 459
Length of database: 405
Length adjustment: 32
Effective length of query: 427
Effective length of database: 373
Effective search space:   159271
Effective search space used:   159271
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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