GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Azospirillum brasilense Sp245

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>FitnessBrowser__azobra:AZOBR_RS25595
          Length = 358

 Score =  391 bits (1004), Expect = e-113
 Identities = 210/359 (58%), Positives = 256/359 (71%), Gaps = 5/359 (1%)

Query: 1   MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60
           MA VTLR +RK++   EV+  ++L++ADGEFV FVGPSGCGKSTL+R+IAGLE+ SGGDL
Sbjct: 1   MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60

Query: 61  TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120
           +I G RVND  PA RGIAMVFQSYALYPHMT YDNMAFGL L+ T K  I   VR AA++
Sbjct: 61  SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120

Query: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180
           L I+ LLDRKP+ LSGGQRQRVAIGRAI R+P+VFLFDEPLSNLDA LRV+MRLE A+L 
Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180

Query: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240
            +L+ TMIYVTHDQVEAMTLAD+IVVL+AG +EQ G+P  LYH P NRFVAGFIGSP MN
Sbjct: 181 ADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMN 240

Query: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISAR 300
           F++ V + +T   V V    G    +AV+ AA   G  +T+G+RPEH+ +     G+ A 
Sbjct: 241 FLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLADGGAGLLAT 300

Query: 301 TMAVESLGDAAYLYAESSVAPDG--LIARIPPLERHTKGETQKLGATPEHCHLFDSAGK 357
            +AVE LG   + +A      DG  L+ R+        GE  +L    E  HLF   G+
Sbjct: 301 ILAVERLGGETHCHA---ALEDGQRLLVRLDGDRPVAAGERLRLNLRGETAHLFGPDGQ 356


Lambda     K      H
   0.320    0.135    0.384 

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: 450
Number of extensions: 18
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: 369
Length of database: 358
Length adjustment: 29
Effective length of query: 340
Effective length of database: 329
Effective search space:   111860
Effective search space used:   111860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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