GapMind for catabolism of small carbon sources

 

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

Align MFS transporter (characterized, see rationale)
to candidate Echvi_3106 Echvi_3106 Sugar phosphate permease

Query= uniprot:A0A166QG26
         (467 letters)



>FitnessBrowser__Cola:Echvi_3106
          Length = 441

 Score =  277 bits (709), Expect = 4e-79
 Identities = 154/470 (32%), Positives = 245/470 (52%), Gaps = 58/470 (12%)

Query: 11  RIGQAVGNYRWTICALLFFATTVNYLDRQVLSLLAPD---------------LSTQF-GW 54
           ++   +  YRW I ALLF AT + Y+DR VLS    D               LS++  G 
Sbjct: 5   KLNSIIKGYRWRIVALLFLATAIKYIDRNVLSFTMIDEGFRREMLGVSDTTALSSELIGK 64

Query: 55  SNSDYANIASVFQFVYAISMLFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGI 114
                  + + F+F YAI  +  G  +D++  +  Y +AI IWS   ++ AF        
Sbjct: 65  FKILMGYVDASFKFAYAIGFVLMGYFIDRVLVRKGYSIAIAIWSLAGIVTAF-------- 116

Query: 115 GAVSSALGIAMIPVSIAGFMVSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSG 174
             VSS  G++           +R V   GE+ NFP AIK  AE+FPKKERSFATGI+N+G
Sbjct: 117 --VSSFRGLSF----------TRFVFGFGESANFPAAIKTIAEWFPKKERSFATGIYNAG 164

Query: 175 ANVGAILAPICVPLIASLWGWEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYI 234
           ANVG +   + VP +    GW  +F+  G+LG V +  W+ +Y+ P+   ++S  E  +I
Sbjct: 165 ANVGIMATVLIVPALILNLGWRWSFLCTGLLGLVLLACWLLIYKPPKAHPKVSQDEQEHI 224

Query: 235 RSDQVVPVVTRPVPGVADKKVSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQ 294
            +D+        VP        W  LL  +  WA A GKF+TD +WWF+L WLP + ++ 
Sbjct: 225 HADEESEHEAEKVP--------WKDLLKTKGAWAIALGKFLTDPIWWFYLTWLPDFFNSN 276

Query: 295 YGMKGQ----AIVMPLAVLYSMTMIGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPL 350
             ++ +     + +P   +Y  + +GS+  GW    F++ G +    R   +L+ A   +
Sbjct: 277 EALETKLDLTGLALPFIFIYFTSDLGSVFFGWLSGKFINMGWSLNKSRKVTLLLCALLVV 336

Query: 351 LVLLAQPLGYISFWVPVLLIGVGASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGL 410
            ++ A  +  +  +V ++L+ + A+AHQ WS N+FT  SD+FP++ + SVVG+ G+ GG+
Sbjct: 337 PLIFAAKVANV--YVAMVLVALAAAAHQGWSANLFTLSSDIFPKRVVGSVVGLAGMVGGI 394

Query: 411 GGVVMTKIGGWVIDHYKLIGDIHTGYMIMFAICALAYLVAWSVMKALVPR 460
           GG +     G ++        +  GY  +F I + AYL+AW ++  LVP+
Sbjct: 395 GGTIFAAFAGIIL--------VKWGYFPIFIIASSAYLLAWLIIHLLVPK 436


Lambda     K      H
   0.327    0.140    0.449 

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: 659
Number of extensions: 39
Number of successful extensions: 8
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: 467
Length of database: 441
Length adjustment: 33
Effective length of query: 434
Effective length of database: 408
Effective search space:   177072
Effective search space used:   177072
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 (21.7 bits)
S2: 51 (24.3 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