GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Azospirillum brasilense Sp245

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate AZOBR_RS15495 AZOBR_RS15495 ABC transporter ATPase

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__azobra:AZOBR_RS15495
          Length = 360

 Score =  206 bits (525), Expect = 6e-58
 Identities = 118/270 (43%), Positives = 164/270 (60%), Gaps = 4/270 (1%)

Query: 16  GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKL 75
           G+VVA+D+V++ I  GE   + GPSG GK++ +RI AGL+   TG +     +VA   + 
Sbjct: 16  GRVVAVDDVSVTIGAGEIVCLCGPSGCGKSSLLRIAAGLEAVQTGSVRIGGTVVADE-RG 74

Query: 76  IVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLN 135
            VPPE R +G+VFQ +AL+P+L+  +N+ F LT   +S E  RKR  E    + +    +
Sbjct: 75  AVPPERRGVGLVFQDYALFPHLSVLDNVRFGLT--ALSGEAQRKRALETLGQVGMAGYAD 132

Query: 136 HFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLL 195
            FP  LSGGQQQRVALARAL  +P++LLLDEPFS LDAR+R+  R     V  + G   +
Sbjct: 133 SFPHHLSGGQQQRVALARALAPNPAVLLLDEPFSGLDARLREQVRDETLHVLKQNGAATM 192

Query: 196 VVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEG 255
           +V+HDP +   +ADR+ ++  GK+VQVG P DLY  PV+   A   GE+N L G V    
Sbjct: 193 LVTHDPEEAMFLADRIALMRAGKVVQVGNPVDLYTRPVNAFAAEFFGEVNRLSGVVQGGA 252

Query: 256 VVIGSLRFPVSVSSDRAI-IGIRPEDVKLS 284
           V       P  V+   A+ + IRPE +KLS
Sbjct: 253 VDTPVGPIPTEVADGTAVDVLIRPEALKLS 282


Lambda     K      H
   0.319    0.139    0.390 

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: 310
Number of extensions: 16
Number of successful extensions: 3
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: 353
Length of database: 360
Length adjustment: 29
Effective length of query: 324
Effective length of database: 331
Effective search space:   107244
Effective search space used:   107244
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 (21.7 bits)
S2: 49 (23.5 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