GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Burkholderia phytofirmans PsJN

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate BPHYT_RS08805 BPHYT_RS08805 sulfate ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__BFirm:BPHYT_RS08805
          Length = 352

 Score =  212 bits (539), Expect = 1e-59
 Identities = 121/310 (39%), Positives = 184/310 (59%), Gaps = 16/310 (5%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I V+N+ K F  G  VALDNV+++   GE   +LGPSG GKTT +R+IAGL+    G++ 
Sbjct: 3   ITVRNLQKRF--GDFVALDNVSLDFPPGELVALLGPSGCGKTTLLRVIAGLEYADGGQVV 60

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEE-----IR 118
              + VA+ G       +R++G VFQ +AL+ ++T FEN+AF L  +K  KE      IR
Sbjct: 61  LQGQDVATVGA-----REREVGFVFQHYALFRHMTVFENVAFGL-RVKPRKERPSEAVIR 114

Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178
           ++V E+ K++ +  +   +P ELSGGQ+QR+ALARAL  +P +LLLDEPF  LDA++R  
Sbjct: 115 EKVHELLKLVQLDWLAQRYPSELSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKE 174

Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238
            R+ ++ +   L ++ + V+HD  +   +ADR+ VL +G + QVG P+D+YD+P +  V 
Sbjct: 175 LRSWLRRLHDDLHISTIFVTHDQEEALEVADRIVVLNRGHVEQVGSPQDVYDHPQTSFVY 234

Query: 239 SLIGEINELEGKVTNEGVVIGSLRFPVSVSSD---RAIIGIRPEDVKLSKDVIKDDSWIL 295
             +G  N L G V   G V+     PVS+ +D    A   +RP D++L          I+
Sbjct: 235 EFLGAANRLHGNVDASGFVVDGAALPVSIKADFSGPAFAYVRPHDLQLYPQASGHREGIV 294

Query: 296 VGKGKVKVIG 305
           V   +V  +G
Sbjct: 295 VDVRRVVTLG 304


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: 308
Number of extensions: 11
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: 352
Length adjustment: 29
Effective length of query: 324
Effective length of database: 323
Effective search space:   104652
Effective search space used:   104652
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