GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_25890
         (276 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28580
          Length = 280

 Score =  153 bits (386), Expect = 5e-42
 Identities = 93/277 (33%), Positives = 147/277 (53%), Gaps = 8/277 (2%)

Query: 7   RRLQSLLLGTLAWA-IAILIF---FPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYLHV 62
           R L+  LL    W  IAIL+    FP ++ ++TS K     F     +I  P   NY  V
Sbjct: 4   RLLKKALLRLGFWCLIAILLVYAVFPFYYAIVTSLKPSSALFQVS-YWIDQPDFSNYAAV 62

Query: 63  NERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVG 122
             ++ +     NS+V++    AL L +++ AAY++   + +     L+ +L   M P V 
Sbjct: 63  LNQASFLRAIGNSLVVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGVSMFPQVA 122

Query: 123 VLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATLW 182
           VL  ++ + ++ GL +T  ALI+ YT+  LP  VW++ T+   +P ++ EAA +DGA+ W
Sbjct: 123 VLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPW 182

Query: 183 QEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLT---SSKAAPLTALIASYSSPEGL 239
             + RVLLP+    L +T LL+ I  WNE  ++L  T   S +  P+   + S  SP  L
Sbjct: 183 VTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHEL 242

Query: 240 FWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276
            W  L A S L   P++I   I Q+++V GL+ GA+K
Sbjct: 243 PWGLLMAASVLVTVPLVILVLIFQRRIVSGLTAGALK 279


Lambda     K      H
   0.327    0.138    0.431 

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: 219
Number of extensions: 9
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: 276
Length of database: 280
Length adjustment: 25
Effective length of query: 251
Effective length of database: 255
Effective search space:    64005
Effective search space used:    64005
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: 47 (22.7 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