GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas putida KT2440

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate PP_1777 PP_1777 phosphomannomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>FitnessBrowser__Putida:PP_1777
          Length = 453

 Score =  583 bits (1504), Expect = e-171
 Identities = 280/450 (62%), Positives = 349/450 (77%), Gaps = 1/450 (0%)

Query: 2   PMTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSA 61
           P+    FKAYDIRG+VP +LNED+A RIG AL A+L     V+G D+RL SP L +AL  
Sbjct: 4   PIQTRCFKAYDIRGQVPADLNEDIAYRIGRALVAELGGRSYVVGRDMRLESPTLSQALMR 63

Query: 62  GLRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSD 121
           GL   G DVIDIGLCGTEEVYF T + +A GG+MVTASHNP  YNGMKLVREQ+RPIS D
Sbjct: 64  GLTEGGADVIDIGLCGTEEVYFATSHYQADGGIMVTASHNPKGYNGMKLVREQSRPISGD 123

Query: 122 TGLFAIRDTVAADTAAPGEPTA-SEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGG 180
           TGL  IR  V +       P A S +  +DK+AY++HLL+YVD +TLKPLK++ + GNG 
Sbjct: 124 TGLKDIRQRVESGDLGTAAPAAGSVRLASDKSAYIDHLLTYVDLATLKPLKVLADPGNGA 183

Query: 181 AGLIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDG 240
            G +++LL   LP +   +  EPDGNFPNGIPNPLLPENRD T +AV D GAD GIA+DG
Sbjct: 184 VGPVLELLKARLPLKLTVINGEPDGNFPNGIPNPLLPENRDLTRQAVLDTGADMGIAFDG 243

Query: 241 DFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVL 300
           DFDRCFFFD+ GRFIEGYY+VGLLA+ +LAK PG K++HDPRLTWNT++QVEEAGG+ + 
Sbjct: 244 DFDRCFFFDNQGRFIEGYYVVGLLAEMLLAKHPGSKIIHDPRLTWNTIKQVEEAGGMAIQ 303

Query: 301 CKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLV 360
            K+GHAFIKE+MR+E+AVYGGEMSAHHYFR+FAY DSG IPWLL+A+L+S +G+SL  LV
Sbjct: 304 SKTGHAFIKERMRAEDAVYGGEMSAHHYFRDFAYCDSGNIPWLLVAQLMSVTGKSLGQLV 363

Query: 361 EARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSNT 420
           + R+  FPCSGEIN++V D K ++ +++ HY   +P +D TDGIS +F  WRF+LR SNT
Sbjct: 364 DERIAAFPCSGEINYEVEDVKDTIEKILAHYLPRNPSIDRTDGISVEFADWRFSLRGSNT 423

Query: 421 EPLLRLNVETRGDAALLETRTQEISNLLRG 450
           EPLLRLNVE+RGD AL+E +  +I+ L+RG
Sbjct: 424 EPLLRLNVESRGDQALVERQVAQIAGLIRG 453


Lambda     K      H
   0.319    0.136    0.404 

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: 691
Number of extensions: 19
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: 450
Length of database: 453
Length adjustment: 33
Effective length of query: 417
Effective length of database: 420
Effective search space:   175140
Effective search space used:   175140
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: 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 (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