GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PLT5 in Dyella japonica UNC79MFTsu3.2

Align polyol transporter 5 (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family

Query= CharProtDB::CH_091483
         (539 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0382
          Length = 472

 Score =  174 bits (440), Expect = 9e-48
 Identities = 143/468 (30%), Positives = 223/468 (47%), Gaps = 31/468 (6%)

Query: 40  AILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDW 99
           A  A++   L G+D  V++GA+  ++    +   +IG       + S +G+  AG  +D 
Sbjct: 21  AAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGPLADR 80

Query: 100 IGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSPASS 159
            GR  T+ +A  +    A+  GL      L+  R + GIGVG A +IAP Y AEVSPA  
Sbjct: 81  WGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVSPARV 140

Query: 160 RGFLNSFPEVFINAGIMLGYVSNL--------AFSNLPLKV-GWRLMLGIGAVPSVILAI 210
           RG L S  ++ I  GI    +S+         A   L L +  WR M  +  VP++I   
Sbjct: 141 RGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPALIYGS 200

Query: 211 GVLAMPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVS 270
            VL +PESPR LV +GR+ +AK+VL +  D   E  L     +H  G       D+ Q S
Sbjct: 201 LVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHAL-----QHKLG-------DIAQ-S 247

Query: 271 RRNSHGEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDH 330
            R+ +  G+ R+L       +  V+   I +  FQQ  GI+ +  +S  ++ + G  ++ 
Sbjct: 248 LRSEYRPGL-RDLR-GSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGF-SES 304

Query: 331 QQLLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKK 390
                +V   VV     LVA  L+DRIGR+PLL     GM ++L  +    +    S   
Sbjct: 305 DAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAA 364

Query: 391 VM----WAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSG 446
           +     W  +VA+     YV  F +  GP+ WV   E+FP R+R+   ++      V + 
Sbjct: 365 LSLPAPWG-MVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANF 423

Query: 447 VISISFLPMSKAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDM 494
           +I+ SF P    +    A+ ++   A V+ VF    + ET+G  LE+M
Sbjct: 424 IITSSF-PALSELGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470


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: 703
Number of extensions: 39
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: 539
Length of database: 472
Length adjustment: 34
Effective length of query: 505
Effective length of database: 438
Effective search space:   221190
Effective search space used:   221190
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