GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Histidine, permease component (characterized)
to candidate AO356_00610 AO356_00610 choline ABC transporter permease subunit

Query= reanno::pseudo5_N2C3_1:AO356_09615
         (283 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00610
          Length = 282

 Score =  212 bits (539), Expect = 9e-60
 Identities = 117/254 (46%), Positives = 166/254 (65%)

Query: 17  WVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRKVLATAVI 76
           +VD L  +  DVF  IS  L   I  L   L       ++AI   +A++  RKV  T  +
Sbjct: 17  YVDWLTQHGADVFDAISLALSGTITALTHALLWFNPLALIAIFAFLAYYIQRKVSLTLFV 76

Query: 77  VGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQT 136
                L+  +G W + M+TLA +  ATL+ V+IG+PLGI++A      +++ P+LD+MQT
Sbjct: 77  AFSFLLIFNLGYWQETMETLAQVTFATLVCVIIGVPLGIVAAHRPMFYTLMRPVLDLMQT 136

Query: 137 MPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGANRW 196
           +P+FVYLIP L LFGLG VP + +TV++A    IRLT LGIR V  E+M+A  AFG +R 
Sbjct: 137 VPTFVYLIPTLTLFGLGVVPGLISTVVFAIAAPIRLTYLGIRDVPDELMDAGKAFGCSRR 196

Query: 197 QQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGRGLEA 256
           Q L  ++LP A+PSI AGI Q  M++LSMVVIA+++GA GLG+ V+  + T ++  G EA
Sbjct: 197 QLLSRIELPHAMPSIAAGITQCIMLSLSMVVIAALVGADGLGKPVVNALNTADIAMGFEA 256

Query: 257 GLAIVILAVVIDRI 270
           GLAIV+LA+++DRI
Sbjct: 257 GLAIVLLAIILDRI 270


Lambda     K      H
   0.328    0.142    0.429 

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: 242
Number of extensions: 11
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: 283
Length of database: 282
Length adjustment: 26
Effective length of query: 257
Effective length of database: 256
Effective search space:    65792
Effective search space used:    65792
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: 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