GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Echinicola vietnamensis KMM 6221, DSM 17526

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  164 bits (414), Expect = 4e-45
 Identities = 113/349 (32%), Positives = 190/349 (54%), Gaps = 40/349 (11%)

Query: 6   VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65
           V  VSK +  G + AL++ ++ ++ G    ++G SG+GK++ +RIIAGL+V S G ++  
Sbjct: 6   VSEVSKRYDAGSL-ALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLG 64

Query: 66  DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125
           D+ + +  + +VP  D +I ++ Q + LYPN T  ENIA PL  +   K   ++R  E+ 
Sbjct: 65  DQKILNPAQKLVPGYD-EIQLIHQEYKLYPNSTVEENIARPL--LLYDKAYQKERTAEIL 121

Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185
           ++L +    +  PR+LSGGQQQ+VA+ RAL  +P +LLLDEPFS+LDA  +      +KE
Sbjct: 122 ELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKE 181

Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245
           +   L VT++ V+HD  D   +++ + ++ KGKL+Q G   +++  P S  VA L G +N
Sbjct: 182 IFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFGYLN 241

Query: 246 ELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKL-SKDVIKDDSWILVGKGKVKVI 304
            + G                   ++ A   +RP +VK+ SK  I           K +V+
Sbjct: 242 LIPG-------------------AEEAY--VRPSEVKITSKTSI-----------KAEVV 269

Query: 305 GYQGGLFRITITPLDSEEEIFTYSDHP---IHSGEEVLVYVRKDKIKVF 350
             Q  +    +T    + E+F   D P   ++ G+EV +  +K+++  F
Sbjct: 270 KQQFLIHYNLLTVKLEDSELFWKVDDPSRSVNVGDEVFLDYQKEQLIQF 318


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: 248
Number of extensions: 16
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: 318
Length adjustment: 28
Effective length of query: 325
Effective length of database: 290
Effective search space:    94250
Effective search space used:    94250
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