GapMind for catabolism of small carbon sources

 

Alignments for a candidate for chvE in Nocardiopsis gilva YIM 90087

Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_017618222.1 CDO52_RS18115 sugar ABC transporter substrate-binding protein

Query= TCDB::P25548
         (354 letters)



>NCBI__GCF_002263495.1:WP_017618222.1
          Length = 369

 Score =  167 bits (423), Expect = 4e-46
 Identities = 114/355 (32%), Positives = 180/355 (50%), Gaps = 26/355 (7%)

Query: 7   LMAACAI--GAASFAAPAFAQDKGSVGIAMPTKSSARWID-DGNNIVKQLQEAGYKTDLQ 63
           L A C    G       A  +D   VG+ +P   +AR+   D     + L E   K +L 
Sbjct: 15  LAAGCGTTTGGDGEGGTASVEDGFKVGLLLPESKTARYEKFDKPYFEEALTELCKKCELS 74

Query: 64  Y--ADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNS 121
           Y  AD +   Q +Q E M+T+GV VLV+ ++D  + + ++K A  QG+ V+AYDRL    
Sbjct: 75  YQNADQETAKQQAQAEAMLTEGVDVLVLDAVDAESAAKIVKDAKGQGVPVVAYDRLA--Y 132

Query: 122 GDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVL 181
           G V YY +FDN +VG +Q  ++ + L  ++  G   I +  GSP D NA  F  GA S+L
Sbjct: 133 GGVDYYVSFDNRKVGEVQGKALIEALEKEETAGKGEIVMINGSPTDPNAADFKAGAHSIL 192

Query: 182 KPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSI 241
               + G            +  T  W P  AQ  M+  +++   D  +  V +  DG++ 
Sbjct: 193 DNEAEIGA-----------EYDTPDWSPDRAQTEMEQAITSIGAD-DIVGVYAANDGMAQ 240

Query: 242 GIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNA 301
           G++++LK  G       LP ++GQDAE+  ++ IIAGEQY T++K  R  A+    M  A
Sbjct: 241 GVVAALKSAGV----DELPPITGQDAEIHGIQRIIAGEQYMTVYKAIRPEAETAAKMAVA 296

Query: 302 VMEGKE---PEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQL 353
              G+E    E+  T+      + V + LL P+ VT+EN ++ +V  G+Y  +++
Sbjct: 297 AATGEEYEGGEIGLTEVESGDGEKVQAVLLDPIPVTEENVEETVVSDGFYTIEEI 351


Lambda     K      H
   0.314    0.133    0.372 

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: 351
Number of extensions: 26
Number of successful extensions: 5
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: 354
Length of database: 369
Length adjustment: 29
Effective length of query: 325
Effective length of database: 340
Effective search space:   110500
Effective search space used:   110500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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