GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PLT5 in Kocuria flava HO-9041

Align polyol transporter 5 (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter

Query= CharProtDB::CH_091483
         (539 letters)



>NCBI__GCF_001482365.1:WP_058858199.1
          Length = 482

 Score =  224 bits (571), Expect = 6e-63
 Identities = 142/459 (30%), Positives = 233/459 (50%), Gaps = 22/459 (4%)

Query: 40  AILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDW 99
           +I+A    +L GYD GV++GA+  +  +L +     G++  SL   + +G+ + GR SD 
Sbjct: 30  SIVACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRISDA 89

Query: 100 IGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSPASS 159
            GRR TI+L   +FF G +++  +PNY  L+ GR   G+ VG A  + PV+ AE++P   
Sbjct: 90  WGRRRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAPYEI 149

Query: 160 RGFLNSFPEVFINAGIMLGYVSNLAFSNLPL--KVGWRLMLGIGAVPSVILAIGVLAMPE 217
           RG +    EV I  G +  +V N    N+ +     WR M  I A+P+V L +G+L MPE
Sbjct: 150 RGSIAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLRMPE 209

Query: 218 SPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNSHGE 277
           SPRWLV +GR  +A  VL ++  S   A   L +++H A           + S  N  G 
Sbjct: 210 SPRWLVEKGRHEEALEVL-RSVRSEERAVAELGEVEHVA----------EEESAENRIGL 258

Query: 278 GVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLATV 337
           G      +     + R+M+  IG+   QQ +GI++++ +   +   +G       L+A +
Sbjct: 259 GA-----VLRNKWLIRIMLVGIGLGIAQQLTGINSIMYYGQIVLIESGFSAS-AALIANI 312

Query: 338 AVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVMWAVVV 397
           A GV+      +A  ++DR+ RR   +            +G +  ++++          V
Sbjct: 313 APGVIAVVGGFIALAMMDRLDRRKTFVIGFSLTTTCHLLIGIASVVLEEGNP---LRPFV 369

Query: 398 AIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMSK 457
            +A V+ +V +         WVY SE+FPL +R  G  + +    V +GV+S+ F  +  
Sbjct: 370 ILALVVAFVGSMQTFLNVAVWVYLSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLVD 429

Query: 458 AMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDE 496
           A+   G F+LF G+  +A VF  T +PET+GR LE ++E
Sbjct: 430 AVGITGTFFLFAGVGVLALVFVATQVPETRGRTLEALEE 468


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: 706
Number of extensions: 38
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: 482
Length adjustment: 34
Effective length of query: 505
Effective length of database: 448
Effective search space:   226240
Effective search space used:   226240
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 24 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