GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PLT5 in Pedobacter sp. GW460-11-11-14-LB5

Align polyol transporter 5 (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter

Query= CharProtDB::CH_091483
         (539 letters)



>FitnessBrowser__Pedo557:CA265_RS23325
          Length = 443

 Score =  231 bits (590), Expect = 3e-65
 Identities = 141/465 (30%), Positives = 247/465 (53%), Gaps = 37/465 (7%)

Query: 35  YAFACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAG 94
           Y    ++LA+    L G+D  V+SG++ ++++  ++     G   GSL + +++G   AG
Sbjct: 10  YITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGAMVGCLIAG 69

Query: 95  RTSDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEV 154
             SD  GR+  +++A  +F A ++ M ++PN  F +  RF +GIGVG A M++P+Y AE+
Sbjct: 70  YVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASMLSPMYIAEL 129

Query: 155 SPASSRGFLNSFPEVFINAGIMLGYVSNLAFSNLPLKVGWRLMLGIGAVPSVILAIGVLA 214
           +P   RG L +  ++ I  GI++  + N    N   +  WR M G+GA+PS I  IG+  
Sbjct: 130 APPKFRGRLVAINQLTIVLGILITNLINYTLRNTG-EDAWRWMFGLGAIPSGIFLIGISI 188

Query: 215 MPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNS 274
           +PESPRWLV +G+   A +VL+K  +                   AD   ++ Q  +R S
Sbjct: 189 LPESPRWLVQKGKNEKALKVLNKIGNHE---------------FAADALKNIEQTLQRKS 233

Query: 275 H--GEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQ 332
           +   E ++ ++     PAV    +  IG+  FQQ  GI+ V  ++P++F++ G   D  Q
Sbjct: 234 NVEHESIFNKMYF---PAV----MIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQD-DQ 285

Query: 333 LLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVM 392
           LL TV +G V   F + A FL+D+IGR+PL+L   GG+ +    +     ++      V 
Sbjct: 286 LLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAVLYVLIS---QLLASGSTMVS 342

Query: 393 WAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISF 452
           W ++ AI         +++   P+TWV  SEIFP ++R + ++  ++       V+  +F
Sbjct: 343 WFLLSAI-------GVYAVSLAPVTWVLISEIFPNKVRVKATTWAILCLWGAYFVLVFTF 395

Query: 453 LPMSKAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDEL 497
            P+         FY++  I T+  +  + F+ ET+G+ LE+++++
Sbjct: 396 -PILFDWLKESIFYIYAAICTLGCIGIWKFVKETKGKTLEEIEDI 439


Lambda     K      H
   0.322    0.137    0.410 

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: 650
Number of extensions: 33
Number of successful extensions: 6
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: 539
Length of database: 443
Length adjustment: 34
Effective length of query: 505
Effective length of database: 409
Effective search space:   206545
Effective search space used:   206545
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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