GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS23325 CA265_RS23325 MFS
           transporter
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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