GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04258 in Pseudomonas putida KT2440

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate PP_1016 PP_1016 mannose/glucose ABC transporter, permease protein

Query= reanno::Smeli:SMc04258
         (302 letters)



>FitnessBrowser__Putida:PP_1016
          Length = 302

 Score =  245 bits (625), Expect = 1e-69
 Identities = 122/291 (41%), Positives = 178/291 (61%)

Query: 9   ARPNQWLRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLW 68
           A P   L+    K+   P +   +V F G   WT V SFT S  LP   + G  QY RL+
Sbjct: 10  ASPLDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFLPTYKWAGLAQYARLF 69

Query: 69  AAPRWLVSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTG 128
              RW V+ +NL +FG L +  SL IG +LA L+DQ+IR E   RTI LYP ALS IVTG
Sbjct: 70  DNDRWWVASKNLLLFGGLFIAISLAIGVLLAVLLDQRIRREGFIRTIYLYPMALSMIVTG 129

Query: 129 LVWQWLLNPQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGL 188
             W+WLLNP  G+  ++R  GW  F  D L + + V+Y ++IAA+WQ +G +M + LAGL
Sbjct: 130 TAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGL 189

Query: 189 RGIDEDIWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGP 248
           RG+D  I +AA++DG  + + Y  +++P +R VF + L+I++   +K +DLV A T+GGP
Sbjct: 190 RGVDPSIIRAAQMDGASLPRIYWTVVLPSLRPVFFSALMILSHIAIKSFDLVAAMTAGGP 249

Query: 249 GIASEVPAKYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLEFGGGR 299
           G +S++PA ++Y + F    +G G A++ +ML  +  I+VP+ Y E    R
Sbjct: 250 GYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAILVPYLYSELRSKR 300


Lambda     K      H
   0.329    0.142    0.449 

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: 330
Number of extensions: 16
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: 302
Length of database: 302
Length adjustment: 27
Effective length of query: 275
Effective length of database: 275
Effective search space:    75625
Effective search space used:    75625
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 (21.8 bits)
S2: 48 (23.1 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