GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Sphingomonas laterariae LNB2

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_089217943.1 CHB74_RS02270 sulfate/molybdate ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_900188165.1:WP_089217943.1
          Length = 351

 Score =  196 bits (498), Expect = 8e-55
 Identities = 128/366 (34%), Positives = 195/366 (53%), Gaps = 42/366 (11%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I +  +SK F  G   AL N+N+ IE GE   +LGPSG+GKTT +RIIAGL+ P TG +Y
Sbjct: 3   IKLDTISKNF--GGFTALGNINLEIEPGEFLALLGPSGSGKTTLLRIIAGLEFPDTGRVY 60

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKM----SKEEIRK 119
           +D   +       +   DR +G VFQ +AL+ ++T  +N+AF LT  K     +K  I+ 
Sbjct: 61  YDGDDITD-----LKVADRGVGFVFQHYALFRHMTVADNVAFGLTVRKRRDRPAKSVIQA 115

Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179
           RV+E+  ++ + H+   +P +LSGGQ+QRVALARAL  +P LLLLDEPF  LDAR+R   
Sbjct: 116 RVQELLDLVQLGHLGKRYPAQLSGGQRQRVALARALAVEPRLLLLDEPFGALDARVRKDL 175

Query: 180 RALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVAS 239
           R  ++E+   +G+T + V+HD  +   +ADRV V+  G + Q+  P+ +YD P S  V  
Sbjct: 176 RRWLRELHDSVGLTSIFVTHDQDEALELADRVVVMDHGVIEQIDTPQKIYDEPASAFVFD 235

Query: 240 LIGEINELEGKVTNEGVVIGSLRFPVSVSS-----DRAIIGIRPEDVKLSKDVIKDDSWI 294
            +GE N++   +      +     P+   +       A +  RP D     +++ DD   
Sbjct: 236 FVGESNQVAVTIAGGEARLFDRTLPLPAGTTLPGDGPARLFFRPHDA----EIVADDKAG 291

Query: 295 LV--------GKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEV--LVYVRK 344
           L           G ++V G   GL R+         EI    D P+    +V   + VR 
Sbjct: 292 LAATVTLTRPNSGSIRVEGKLDGLDRLV--------EI----DVPVEGAPQVGERIIVRP 339

Query: 345 DKIKVF 350
            ++K++
Sbjct: 340 TRVKLY 345


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: 317
Number of extensions: 10
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: 351
Length adjustment: 29
Effective length of query: 324
Effective length of database: 322
Effective search space:   104328
Effective search space used:   104328
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 24 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