GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0327 in Halococcus hamelinensis 100A6

Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_007695788.1 C447_RS16060 sugar ABC transporter permease

Query= TCDB::Q72KX3
         (369 letters)



>NCBI__GCF_000336675.1:WP_007695788.1
          Length = 324

 Score =  103 bits (256), Expect = 8e-27
 Identities = 71/206 (34%), Positives = 107/206 (51%), Gaps = 16/206 (7%)

Query: 176 LVVGLVLLYVAYTAYREGERRRALWGLASA------GVLLLWAFAFGQGLRLLPYPEVHG 229
           LV+GL L  V     R  E+ + ++ L  A          LW + +  G+  +    V  
Sbjct: 116 LVLGLALAIVLDRQIRFKEQIQTIYLLPMALSFVVTAQFWLWMYNYNSGVINIILDAVGI 175

Query: 230 FSLALVG--------VILAAVWQMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRR 281
             +  +G        VI A +WQ SGYTM +YL+GL+ IP +  EAA  DGAS  +++ R
Sbjct: 176 GRIQFIGDPRFVLGAVIFALIWQFSGYTMIVYLSGLQSIPQDQFEAAATDGASTVKIYWR 235

Query: 282 VIFPMLAPITLSAMIVLGHIALKIFDLVFAMAGLDYAP--TDVPAIYMYLLAFRGNQFAK 339
           VI P L   ++SA +VL   ALK F  +++M G    P  +D+ A  M   AF+  +++ 
Sbjct: 236 VIIPQLKSASVSAAVVLMIFALKAFTFLYSMFGTYRPPNGSDILATLMVRQAFKFQEWSY 295

Query: 340 GAAIGILLLLLVAVVVVPYLATQLRK 365
            AA+  LLLL+  VV+ PYL  Q ++
Sbjct: 296 AAAVATLLLLMALVVIGPYLYYQYQR 321



 Score = 66.6 bits (161), Expect = 9e-16
 Identities = 49/142 (34%), Positives = 68/142 (47%), Gaps = 20/142 (14%)

Query: 18  VGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYREL-FTGFVDVRFRQSVV 76
           +G FVYG IG NL VSLTD+                 G  +Y +L F  +V       V+
Sbjct: 53  MGFFVYGGIGWNLLVSLTDYTG--------------FGSADYGDLDFEMYVQALSSPDVI 98

Query: 77  ----NLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFVVTGTIWRWL 132
               N     + F A  L LGL LA+ +D+  R +   +T++L PMALSFVVT   W W+
Sbjct: 99  AASRNTFVLLVVFTAVCLVLGLALAIVLDRQIRFKEQIQTIYLLPMALSFVVTAQFWLWM 158

Query: 133 LQPQGGV-NVLPTLFGLPPLSF 153
                GV N++    G+  + F
Sbjct: 159 YNYNSGVINIILDAVGIGRIQF 180


Lambda     K      H
   0.331    0.146    0.458 

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: 299
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 369
Length of database: 324
Length adjustment: 29
Effective length of query: 340
Effective length of database: 295
Effective search space:   100300
Effective search space used:   100300
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: 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