GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Marinobacter adhaerens HP15

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Marino:GFF1380
          Length = 362

 Score =  199 bits (507), Expect = 7e-56
 Identities = 114/320 (35%), Positives = 190/320 (59%), Gaps = 17/320 (5%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I ++ ++K F K +  AL ++N+ I +G+   +LGPSG+GKTT +RIIAGL+ P  G + 
Sbjct: 3   IEIQGINKFFDKFQ--ALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIR 60

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNM----KMSKEEIRK 119
           F  + V       +   DR++G VFQ +AL+ ++T  EN+AF L  +    +  K EIRK
Sbjct: 61  FSGKDVTD-----LHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRK 115

Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179
           RV+++ +++ + H+ + +P +LSGGQ+QR+ALARA+   P +LLLDEPF  LDA++R   
Sbjct: 116 RVKDLLEMVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDL 175

Query: 180 RALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVAS 239
           R  ++ +   L  T + V+HD  +   ++D+V V+  G++ QV  P +LY  P S  V  
Sbjct: 176 RRWLRSLHDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFE 235

Query: 240 LIGEINELEGKVTNEGVVIGS--LRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVG 297
            +G++N L GK+ +  +  G   +R P    +D A + +RP +V+L++    DD+ +   
Sbjct: 236 FLGQVNVLSGKIRDGVMRQGDAWIRLPEGCENDDAQLYLRPHEVRLTQSA-SDDAHL--- 291

Query: 298 KGKVKVIGYQGGLFRITITP 317
             +++ I   G   RI + P
Sbjct: 292 PFRIEAINLIGAEVRIELKP 311


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: 328
Number of extensions: 15
Number of successful extensions: 4
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: 362
Length adjustment: 29
Effective length of query: 324
Effective length of database: 333
Effective search space:   107892
Effective search space used:   107892
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