GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05255 in Pseudomonas fluorescens FW300-N1B4

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= uniprot:D8J112
         (347 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Ribose ABC transport
           system, permease protein RbsC (TC 3.A.1.2.1)
          Length = 325

 Score =  206 bits (523), Expect = 9e-58
 Identities = 123/329 (37%), Positives = 185/329 (56%), Gaps = 10/329 (3%)

Query: 17  NTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVL 76
           NTAS  G R+  F        LA A LL M+  FS  S +F+  D   ++        VL
Sbjct: 2   NTASLAGKRSGNFYGLGTYLGLAGA-LLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVL 60

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

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

Query: 197 AVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIA 256
           A+LI+F+    A  +L +TVFGRY   +G+NEEA+RL+G+    +K+ V++  G + GIA
Sbjct: 176 ALLIIFI----AQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIA 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: 11
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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