GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Pseudomonas putida KT2440

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate PP_2774 PP_2774 glycine betaine ABC transporter, ATPase/permease fusion protein

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Putida:PP_2774
          Length = 698

 Score =  235 bits (600), Expect = 2e-66
 Identities = 117/233 (50%), Positives = 159/233 (68%)

Query: 35  SRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDL 94
           SRS  T  +  V+L +  G++  +MG SGSGKSTL+RH+NRLIEP+SGEVL DG+ +  L
Sbjct: 47  SRSDSTNAVEQVNLAVRRGEVLCLMGTSGSGKSTLLRHVNRLIEPSSGEVLIDGEVLSSL 106

Query: 95  GAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLS 154
               LR  R +R+ MVFQ F L+PHR+VL NV     +RG  +   R   ++ +  VGL 
Sbjct: 107 TQPTLRQLRSQRIGMVFQHFGLLPHRSVLDNVALPLELRGEPESTRRTAALRQLQAVGLK 166

Query: 155 GYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLA 214
            +  +FPH+LSGGM+QRVGLARAL  + D++LMDE FSALDP IR D+Q + LQL R   
Sbjct: 167 AWSERFPHELSGGMQQRVGLARALVTNPDILLMDEPFSALDPTIRRDLQGRFLQLVRERG 226

Query: 215 KTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQRR 267
            T + +THD  EALR+   IA+LR G+++QVGTP ++L++PA++ VA F   R
Sbjct: 227 ITTLLVTHDPGEALRLADRIAVLRGGRLIQVGTPGELLEHPADEGVAVFFDER 279


Lambda     K      H
   0.323    0.139    0.397 

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: 429
Number of extensions: 19
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: 275
Length of database: 698
Length adjustment: 32
Effective length of query: 243
Effective length of database: 666
Effective search space:   161838
Effective search space used:   161838
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 (21.9 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