GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Rhodobacter johrii JA192

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_069332842.1 C8J29_RS18660 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_003046325.1:WP_069332842.1
          Length = 352

 Score =  202 bits (513), Expect = 1e-56
 Identities = 129/346 (37%), Positives = 199/346 (57%), Gaps = 36/346 (10%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  + V+NV K +    +  +++++ +I +GE    +GPSG GK+T +R+IAGL+    G
Sbjct: 1   MSTVHVRNVKKSYSD--LTVIEDLSFDIHDGEFMVFVGPSGCGKSTLLRMIAGLESFQGG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           E+   +R+V  NG   VP  DR I MVFQ +ALYP++T  +N++F L   K    EI +R
Sbjct: 59  EVAIGERVV--NG---VPARDRNIAMVFQDYALYPHMTIRDNMSFGLKMRKTPTAEIERR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V   A+IL I H+L+  PR LSGGQ+QRVA+ RA+V++P + L DEP SNLDA++R   R
Sbjct: 114 VAAAAEILQIGHLLDRKPRALSGGQRQRVAMGRAIVREPDVFLFDEPLSNLDAKLRVEVR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +K + +RLG T++ V+HD  +   +ADR+ VL  G + Q+G P++LY  P +  VA  
Sbjct: 174 TEIKRLHARLGATMIYVTHDQVEAMTMADRIVVLKGGAVEQIGTPQELYREPRTRFVAGF 233

Query: 241 IGE--INELEGKVTNE-GVVIGSLRFPVS--VSSDRAI---IGIRPEDVKLSK------- 285
           IG   +N    ++  +   ++   R PV    S  RA+   IGIRPE V+L+        
Sbjct: 234 IGSPGMNFAPARIEGDVATLVTGDRVPVRRLSSGTRAVQGEIGIRPEHVQLADPHGPGVE 293

Query: 286 ---DVIKD---DSWILVGKGKV--------KVIGYQGGLFRITITP 317
              DV++    D+ + V  G+         ++I  +G   R++ TP
Sbjct: 294 TLVDVVEPLGADTLVAVRLGEAQLMVRLPGEIIPAEGDRLRLSFTP 339


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: 265
Number of extensions: 13
Number of successful extensions: 2
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 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