GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacG in Desulfovibrio vulgaris Miyazaki F

Align LacG, component of Lactose porter (characterized)
to candidate 8499893 DvMF_0658 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::P29824
         (273 letters)



>FitnessBrowser__Miya:8499893
          Length = 277

 Score =  116 bits (290), Expect = 6e-31
 Identities = 63/198 (31%), Positives = 112/198 (56%), Gaps = 1/198 (0%)

Query: 73  NSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAALMIPLFMLMGQ 132
           N+V +  +  A  L++ +LA Y F  +    +  ++ ++L+ LM+    L++  +  M  
Sbjct: 75  NTVLLVTMVLAGQLVLCTLAAYAFAKYDFPGKGILFALVLMQLMIMPDVLVVENYRTMSA 134

Query: 133 AGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQIFFYIYVPVMRS 192
            G+L++ +AI LP +ASAF IF  RQ  K+ P EL +AA V+G    QI + +YVP+ + 
Sbjct: 135 IGVLDSTLAIGLPYMASAFGIFLLRQTFKSIPKELDEAAAVEGASTLQILWKVYVPLGKP 194

Query: 193 TYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASA-YSPEYGTVMIGTILATL 251
            Y A  ++    +WNN+LWPLIV  + +++ +T+ +   +S     ++  +   T++ + 
Sbjct: 195 VYLAYALVSVSYHWNNFLWPLIVTNTTNSRPLTVGLQVFSSTEQGVDWSIITAATLMTSG 254

Query: 252 PTLLVFFAMQRQFVQGML 269
           P L+ F   QRQFVQ  +
Sbjct: 255 PLLIGFLLFQRQFVQSFM 272


Lambda     K      H
   0.331    0.140    0.416 

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: 217
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: 273
Length of database: 277
Length adjustment: 25
Effective length of query: 248
Effective length of database: 252
Effective search space:    62496
Effective search space used:    62496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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