GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Dechlorosoma suillum PS

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  193 bits (491), Expect = 5e-54
 Identities = 117/351 (33%), Positives = 191/351 (54%), Gaps = 37/351 (10%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I ++N++K F  G  VALD+V+++I  GE   +LGPSG GKTT +RIIAG++    G++ 
Sbjct: 3   IEIRNIAKRF--GNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVM 60

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKE-----EIR 118
           F+           +   +R++G VFQ +AL+ ++  FEN+AF L  +K  KE     EIR
Sbjct: 61  FEGSEATH-----LHARERQVGFVFQHYALFRHMNVFENVAFGL-RVKPRKERPCESEIR 114

Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178
           KRV ++  ++ +  + + +P +LSGGQ+QR+ALARAL  +P +LLLDEPF  LD ++R  
Sbjct: 115 KRVMDLLSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKE 174

Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVA 238
            R  ++ +   + ++ + V+HD  +   +ADRV V+ KG++ QVG P+++Y NP S  V 
Sbjct: 175 LRRWLRRLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVY 234

Query: 239 SLIGEINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGK 298
             +G +N    +V      +     P   +   A+  IRP D+ +      +       +
Sbjct: 235 QFLGNVNVFHSRVHGAWAEVARDDVP---AGQEAVAFIRPHDIDIDTVATPESL-----E 286

Query: 299 GKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRKDKIKV 349
            KV  +   G L R+ +                IH GE V V + +++ +V
Sbjct: 287 AKVSYVQTIGPLVRVEV----------------IHQGELVEVELTRERQQV 321


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: 322
Number of extensions: 13
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