GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21219 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate AO356_27680 AO356_27680 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21219
         (281 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27680
          Length = 276

 Score =  133 bits (335), Expect = 4e-36
 Identities = 86/282 (30%), Positives = 147/282 (52%), Gaps = 10/282 (3%)

Query: 1   MERQSPLFSVFIHASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRT 60
           +++   L S+ +   A  +A++I  P+ W+++ S     D  A P    P  I       
Sbjct: 3   LQQSRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATP----PQFIFTPTLEN 58

Query: 61  LLSAVENSAGAAFIASLLNSIKVAGMATLAAVVVAVPAAWAVS--RTPAVAWSLYAVIAT 118
            L   E S   +F     NS+ ++  AT   +++AVPAA++++   T     +L  +++T
Sbjct: 59  YLHINERSNYFSFA---WNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLST 115

Query: 119 YMLPPVALAVPLYMGLAYFGLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAM 178
            MLPPV + +P+Y+    FGLL++   L ++Y  I  P   W++ + F  IPR+I  AA 
Sbjct: 116 KMLPPVGVLMPIYLLAKQFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPRDILEAAR 175

Query: 179 IDGARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLA 238
           +DGA L Q +  + LP+A   +A++ L + +L W+E F++L  TS  +A  LT  IA  +
Sbjct: 176 LDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTS-SKAAPLTALIASYS 234

Query: 239 GGRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVK 280
                 +  ++    LA  P ++ G I Q+ L+ GL+ G VK
Sbjct: 235 SPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276


Lambda     K      H
   0.325    0.136    0.402 

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: 218
Number of extensions: 8
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: 281
Length of database: 276
Length adjustment: 25
Effective length of query: 256
Effective length of database: 251
Effective search space:    64256
Effective search space used:    64256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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