GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Sinorhizobium meliloti 1021

Align ABC transporter permease (characterized, see rationale)
to candidate SM_b21459 SM_b21459 sugar uptake ABC transporter permease

Query= uniprot:A0A166QFV1
         (320 letters)



>FitnessBrowser__Smeli:SM_b21459
          Length = 297

 Score =  313 bits (803), Expect = 2e-90
 Identities = 153/293 (52%), Positives = 211/293 (72%), Gaps = 8/293 (2%)

Query: 21  VQRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNG 80
           ++R++ R AW+FL P+LL L  VA WPL R+ +FS TDA L       F+G  N++    
Sbjct: 7   MERQQRRTAWIFLLPLLLTLMAVAIWPLARSIFFSFTDAYLDAPSDYGFVGIENFV---- 62

Query: 81  SSWSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWA 140
                +  DP +W AVRNTL FT+VSVGLE +LGL +ALLL+  F GR +VRA ILIPWA
Sbjct: 63  ----EVAEDPVFWGAVRNTLVFTLVSVGLETLLGLAIALLLHRAFLGRGIVRAAILIPWA 118

Query: 141 IPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFV 200
           +P +VSA+IW WMLNDQFG+IN L+++LGL++  +AWTAD  L +  VI +DVW T PF+
Sbjct: 119 MPMVVSARIWEWMLNDQFGLINKLLVALGLVEKGVAWTADPSLILGTVIFIDVWVTTPFM 178

Query: 201 TLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVI 260
            LL+LA LQ++P + YEAA V G+   K FW +TLPL  PA+ VA +FR LD+LR+FD+ 
Sbjct: 179 VLLILAGLQLIPEEIYEAADVSGVPQWKRFWSITLPLATPAIGVAILFRTLDALRMFDLS 238

Query: 261 YVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGR 313
           YVL +N+ +TM+MS+YAR  L+ FQD+G G+AAST +F+++ +IA++ + L R
Sbjct: 239 YVLAANNENTMTMSIYARDQLISFQDLGLGAAASTWVFMIIGLIAIVIVGLLR 291


Lambda     K      H
   0.329    0.140    0.443 

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: 291
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: 320
Length of database: 297
Length adjustment: 27
Effective length of query: 293
Effective length of database: 270
Effective search space:    79110
Effective search space used:    79110
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.

Links

Downloads

Related tools

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