GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5404 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate AO353_16280 AO353_16280 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_16280 AO353_16280 amino acid
           ABC transporter permease
          Length = 223

 Score =  136 bits (343), Expect = 5e-37
 Identities = 73/217 (33%), Positives = 122/217 (56%), Gaps = 7/217 (3%)

Query: 146 GLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVP 205
           G+       W G+++TL +  +G+VG + LG +LAL R S+   +  +   ++ ++R +P
Sbjct: 7   GVVQAVPGMWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIP 66

Query: 206 LITVLFMSSVMLPLFLP----EGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQY 261
           L+ V+    + +P  L     E          ++  ++F++AY  E+VR G+Q+IPKGQ 
Sbjct: 67  LLLVITWFYLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQM 126

Query: 262 EAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAA 321
            AA A+G+GY + M L+ILPQA + + P ++   I LF+DTSLV  +GL D LN+ +   
Sbjct: 127 GAAKALGMGYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATR--- 183

Query: 322 ADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERK 358
           A    +G A E  + A LV++   F  SR    L+++
Sbjct: 184 ASGDIIGRANEFLIIAGLVYFTISFAASRLVKRLQKR 220


Lambda     K      H
   0.330    0.144    0.469 

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: 273
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: 365
Length of database: 223
Length adjustment: 26
Effective length of query: 339
Effective length of database: 197
Effective search space:    66783
Effective search space used:    66783
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 (21.9 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 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