GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family

Query= TCDB::P15729
         (468 letters)



>FitnessBrowser__Cola:Echvi_2810
          Length = 450

 Score =  248 bits (633), Expect = 3e-70
 Identities = 152/448 (33%), Positives = 240/448 (53%), Gaps = 28/448 (6%)

Query: 23  VAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSV-SLALLGSALGAFGAGPIADRH 81
           + +L GFLFGFDTAVI+GA   L+  +QT     G  + S+AL G+ +GA   G      
Sbjct: 11  IVSLTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHL 70

Query: 82  GRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEVSPAHLR 141
           GR  T+    V+F +S++G+ L    + F F+R +GG+ +GA+S+ AP Y++E+S A+ R
Sbjct: 71  GRKNTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQR 130

Query: 142 GRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIPALLYGV 201
           GR   L Q+ IVSGI +A +SN+   L+ G    N        WRWM   E+IPA++Y  
Sbjct: 131 GRRVGLYQINIVSGILVAYVSNY---LLQGVGDHND-------WRWMLAAEIIPAIIYLA 180

Query: 202 CAFLIPESPRYLVAQGQGEKAA-AILWKVEGGDVPSRIEEIQATVSLDHKPRFSDLLSRR 260
               IPESPR+L+ + + E AA  +L K+  G +   +  I+       K +     +R 
Sbjct: 181 FILDIPESPRWLILKQKDESAAQKVLKKITTGKIDQLLLSIKHDSLRSKKMKLFSAKNR- 239

Query: 261 GGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGFINILTTLV 320
              LP+   G+ ++   Q  GIN I YY+  +    GF    SLL  V  GF N++ TL+
Sbjct: 240 ---LPLFLAGI-IAIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLI 295

Query: 321 AIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIALVTANLYV 380
            ++ +DK GRK L+L+GS+G  I+LG++S  F              ++ +  L +  +++
Sbjct: 296 GMSLIDKTGRKQLMLIGSMGYIISLGLVSYGF-----------YDSSSPLFILTSILIFI 344

Query: 381 FSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDTVGLGPAYG 440
            + G   G ++WV + E+F NK+RA   S  AGV W    +I+     L+DT+     + 
Sbjct: 345 AAHGIGQGAVIWVFISEIFPNKVRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIFM 404

Query: 441 LYATSAAISIFFIWFFVKETKGKTLEQM 468
           ++     +   F+W ++ ETKG  LE +
Sbjct: 405 VFMALMILQFVFVWRYMPETKGLELENL 432


Lambda     K      H
   0.325    0.140    0.430 

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: 580
Number of extensions: 29
Number of successful extensions: 5
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: 468
Length of database: 450
Length adjustment: 33
Effective length of query: 435
Effective length of database: 417
Effective search space:   181395
Effective search space used:   181395
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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