GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Pedobacter sp. GW460-11-11-14-LB5

Align D-xylose-proton symporter (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter

Query= CharProtDB::CH_109760
         (491 letters)



>FitnessBrowser__Pedo557:CA265_RS23325
          Length = 443

 Score =  313 bits (802), Expect = 8e-90
 Identities = 183/476 (38%), Positives = 271/476 (56%), Gaps = 45/476 (9%)

Query: 3   TQYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVA 62
           +++N++YI  I+L+A  GG LFG+D AVISG++  L   F               GF   
Sbjct: 4   SKFNTAYITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWE--------GFATG 55

Query: 63  SALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAW-PELGFTSINPDNTVPVY 121
           S  +G ++G  + GY S+ +GR+  L IAA +F  S +  A  P   F            
Sbjct: 56  SLALGAMVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDF------------ 103

Query: 122 LAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCV 181
                  F++ R   GIGVG+ASMLSPMYIAELAP   RG+LV+ NQ  I+ G L+   +
Sbjct: 104 -------FIVSRFFSGIGVGMASMLSPMYIAELAPPKFRGRLVAINQLTIVLGILITNLI 156

Query: 182 NYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR 241
           NY +  +G+      D WR+MF    IP+ +FL+ +  +PESPRWL+ +GK E+A  +L 
Sbjct: 157 NYTLRNTGE------DAWRWMFGLGAIPSGIFLIGISILPESPRWLVQKGKNEKALKVLN 210

Query: 242 KIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGV--GVIVIGVMLSIFQQFVGINVVLYY 299
           KI  +  A  A++ I+ +L          +   +    ++IG+ L+IFQQF GIN V  Y
Sbjct: 211 KIGNHEFAADALKNIEQTLQRKSNVEHESIFNKMYFPAVMIGIGLAIFQQFCGINTVFNY 270

Query: 300 APEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSL 359
           AP++F+++G S D  LLQT+ +G +N+ FT+ A+  VDK GRKPL +IGA G+A+ ++ L
Sbjct: 271 APKLFESIGTSQDDQLLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAV-LYVL 329

Query: 360 GTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419
            +        +V+   +L  +  +A+S  PV WVL+SEIFPN +R KA   A+   W A 
Sbjct: 330 ISQLLASGSTMVSWF-LLSAIGVYAVSLAPVTWVLISEIFPNKVRVKATTWAILCLWGAY 388

Query: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELE 475
           + + +TFP++    WL         ++IY  +  L  + +WKFV ETKGKTLEE+E
Sbjct: 389 FVLVFTFPIL--FDWLKESI-----FYIYAAICTLGCIGIWKFVKETKGKTLEEIE 437


Lambda     K      H
   0.326    0.140    0.433 

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: 583
Number of extensions: 33
Number of successful extensions: 7
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: 491
Length of database: 443
Length adjustment: 33
Effective length of query: 458
Effective length of database: 410
Effective search space:   187780
Effective search space used:   187780
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