GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Pseudomonas fluorescens GW456-L13

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910
          Length = 325

 Score =  204 bits (520), Expect = 2e-57
 Identities = 123/329 (37%), Positives = 186/329 (56%), Gaps = 10/329 (3%)

Query: 17  NTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVL 76
           NTAS  G R+  F        LA A LL MI+ FS  S +F+  D   ++        VL
Sbjct: 2   NTASYAGKRSGNFYGLGTYLGLAGA-LLAMIVLFSVLSSHFLSYDTFSTLANQIPDLMVL 60

Query: 77  AIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMV 136
           A+  T+V+I  GIDLSVG+++   A    V +  WG  +       +   AL+G I+G +
Sbjct: 61  AVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSI 120

Query: 137 IAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPN 196
               ++P FI +LG++ + +G++  ++G+R  Y  D   F+ ++     G + PS  I  
Sbjct: 121 TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDA--FAWLSNPIAFG-ISPSFII-- 175

Query: 197 AVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIA 256
           A+LI+F+    A  +L +TVFGRY   +G+NEEA+RL+G+    +KV V++  G + G+A
Sbjct: 176 ALLIIFV----AQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKVLVFSLMGLLAGVA 231

Query: 257 GLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRI 316
            L   SRL +A P  G G EL  IAAVVIGGTSL GG G+++ T  G  I+SVL  GL  
Sbjct: 232 ALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQ 291

Query: 317 MSVAQEWQTVVTGVIIILAVYLDILRRRR 345
           +   +  + ++TG +I++AV LD  R +R
Sbjct: 292 IGATEPTKRIITGAVIVVAVVLDTYRSQR 320


Lambda     K      H
   0.326    0.139    0.398 

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: 245
Number of extensions: 14
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: 347
Length of database: 325
Length adjustment: 28
Effective length of query: 319
Effective length of database: 297
Effective search space:    94743
Effective search space used:    94743
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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