GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Pseudomonas putida KT2440

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PP_2760 PP_2760 putative ribose transport permease protein

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__Putida:PP_2760
          Length = 327

 Score =  133 bits (335), Expect = 6e-36
 Identities = 107/325 (32%), Positives = 162/325 (49%), Gaps = 21/325 (6%)

Query: 25  AQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMT 84
           AQWLL R  +L    +L      L   LS     NF +  N +N+L Q AI   LA G+T
Sbjct: 15  AQWLLRRGALLAFAAIL------LAFALSAP---NFLTLSNLVNVLAQSAILGSLAFGLT 65

Query: 85  FVIL-------TAGIDLSVGSVLAVSAVLGMQVS-LGAAPGWAIPMFIFSGLVMGMVNGA 136
            VI+       + G+DLS+ + L +SA +   ++  G     +I   + +GL +G +N  
Sbjct: 66  TVIIGGGSNVVSGGLDLSLAANLGLSAAVYASLNNAGFGDVVSIAATLGTGLAIGTLNAL 125

Query: 137 MVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAV 196
           +V    +   + TL TM    G   +L + T VL +  P  E +  G ++ VP L WV +
Sbjct: 126 VVVGFRLPPLLATLATMNLVAGLELVLTENT-VLPSTSPLLEGLAFGSWVGVPALAWVLL 184

Query: 197 AVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSAS 256
           AV  +  V+ + T  G+ +YAIG   +AA   G+ V   +   Y ISGL   LA   SA+
Sbjct: 185 AVGGVLIVLTQYTPFGLRLYAIGEYPEAANAAGLSVRGYVFASYLISGLCGSLAAFCSAA 244

Query: 257 RLYGANGNWGSGYELDAIAAVVLGGTSLMGGV-GSIWGTVVGALIIGVMNNGLTILGLSS 315
              G+    GSG  L ++ A+   G      +  SI GT++  L++GV+ NG  +L +SS
Sbjct: 245 WFSGS--TTGSGEMLLSVVAIAFLGVIFSQRLQPSIGGTLLATLLVGVLINGFQLLNISS 302

Query: 316 FWQYVAKGAVIVLAVILDKWRQKDA 340
           FW    +G +I+L V L   R K+A
Sbjct: 303 FWVDGVQGVLILLVVALSGLRNKEA 327


Lambda     K      H
   0.324    0.138    0.417 

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: 304
Number of extensions: 12
Number of successful extensions: 3
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: 344
Length of database: 327
Length adjustment: 28
Effective length of query: 316
Effective length of database: 299
Effective search space:    94484
Effective search space used:    94484
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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