GapMind for catabolism of small carbon sources

 

Alignments for a candidate for STP6 in Dyella japonica UNC79MFTsu3.2

Align sugar transport protein 6 (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family

Query= CharProtDB::CH_091493
         (507 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0382
          Length = 472

 Score =  187 bits (474), Expect = 9e-52
 Identities = 147/491 (29%), Positives = 232/491 (47%), Gaps = 56/491 (11%)

Query: 14  EAKMTVYVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCK 73
           E + T  V +    AA+GG +FG+D  +  G  A+D     F                  
Sbjct: 10  EGRATARVVLIAAAAALGGFLFGFDTAVING--AVDAVRGSFGLGAGR------------ 55

Query: 74  YDNQFLQLFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLI---GVGLTAGAVNL 130
                +    S   L + + ++ A     + GR  TMQ A++   I   G GL AG  +L
Sbjct: 56  -----IGFAVSCALLGSALGAWYAGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDL 110

Query: 131 VMLIIGRLFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTA 190
           V+    RL  G GVG  +   P +++E++PA++RG L  + QL + +GI  A + + + A
Sbjct: 111 VLW---RLVGGIGVGVASVIAPTYIAEVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLA 167

Query: 191 TVHP----------YGWRIALGGAGIPAVILLFGSLL--IIETPTSLIERNKNEEGKEAL 238
                           WR     A +PA  L++GSL+  + E+P  L+ + + +E K+ L
Sbjct: 168 GTAGGASQKLWLGLEAWRWMFLVAVVPA--LIYGSLVLGVPESPRHLVAKGRMDEAKQVL 225

Query: 239 RKIRGVDDINDEYESIVHACDIASQVKDPYRKLLKPASR------PPFIIGMLLQLFQQF 292
           R++    D+ DE+       DIA  ++  YR  L+          P   +G+LL +FQQF
Sbjct: 226 RQVL---DLQDEHALQHKLGDIAQSLRSEYRPGLRDLRGSMAGLLPVVWVGILLSVFQQF 282

Query: 293 TGINAIMFYAPVLFQTVGFGSDAALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSV 352
            GIN I +Y+  L+ +VGF    A   +V+T  +NVL T V I LVDR GR+ LL   S 
Sbjct: 283 VGINVIFYYSSTLWHSVGFSESDAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSA 342

Query: 353 HMLICQLIIG--IILAKDLGVTGTLGRPQALVVVIFVCVYVMGFAWSWGPLGWLIPSETF 410
            M +   ++      A   G   +L  P  +V ++    YV+ F  SWGP+ W++  E F
Sbjct: 343 GMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVALVAANAYVVFFGLSWGPMVWVLLGEMF 402

Query: 411 PLETRSAGFAVAVSCNMFFTFVIAQAF--LSML-CGMRSGIFFFFSGWIIVMGLFAFFFI 467
           P   R+   AVA +      F+I  +F  LS L      G++ FF+   +V  +F    +
Sbjct: 403 PNRIRAIALAVAAAAQWVANFIITSSFPALSELGLSFAYGVYAFFA---LVSLVFVVKAV 459

Query: 468 PETKGIAIDDM 478
            ETKG+ +++M
Sbjct: 460 RETKGMELEEM 470


Lambda     K      H
   0.329    0.144    0.446 

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: 585
Number of extensions: 39
Number of successful extensions: 8
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: 507
Length of database: 472
Length adjustment: 34
Effective length of query: 473
Effective length of database: 438
Effective search space:   207174
Effective search space used:   207174
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 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