GapMind for catabolism of small carbon sources

 

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

Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter

Query= reanno::Korea:Ga0059261_1777
         (458 letters)



>NCBI__GCF_001482365.1:WP_058858199.1
          Length = 482

 Score =  211 bits (537), Expect = 4e-59
 Identities = 133/432 (30%), Positives = 219/432 (50%), Gaps = 11/432 (2%)

Query: 29  AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88
           A  GGLLFG+DT VI+GA + +  + GLT    G   +S +    +G+L  G  +D +GR
Sbjct: 33  ACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRISDAWGR 92

Query: 89  KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148
           +  +L +A+ + V ++     P+    +  R   GLA+G AS V P+++AE++P   RG 
Sbjct: 93  RRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAPYEIRGS 152

Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGL-VQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPR 207
           +   N++ IV+G L AF+ N +I  + + +   WR+MF I A+P+    +  L +PESPR
Sbjct: 153 IAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLRMPESPR 212

Query: 208 WLAIHGQADRARDVMQRLGFADPR-AELARIELAEAREEAAGK----PRLFQRSHFTPVA 262
           WL   G+ + A +V++ +   +   AEL  +E     E A  +      L  +     + 
Sbjct: 213 WLVEKGRHEEALEVLRSVRSEERAVAELGEVEHVAEEESAENRIGLGAVLRNKWLIRIML 272

Query: 263 CAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRF 322
             I + +  QL+GIN+++YY   +   +G  A +AL+ +IA G   +V    AL ++DR 
Sbjct: 273 VGIGLGIAQQLTGINSIMYYGQIVLIESGFSASAALIANIAPGVIAVVGGFIALAMMDRL 332

Query: 323 GRRPLLFVGSVICAATLLLVGWQ---LESAKPDGTLILFGL-LGFIAAFAMSQGAVIWVF 378
            RR    +G  +     LL+G     LE   P    ++  L + F+ +        +WV+
Sbjct: 333 DRRKTFVIGFSLTTTCHLLIGIASVVLEEGNPLRPFVILALVVAFVGSMQTFLNVAVWVY 392

Query: 379 ISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTW 437
           +SEVFP  +RG G  +     WV    ++  FP    +VG    F  F  + +L L++  
Sbjct: 393 LSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLVDAVGITGTFFLFAGVGVLALVFVA 452

Query: 438 KFMPETNGIALE 449
             +PET G  LE
Sbjct: 453 TQVPETRGRTLE 464


Lambda     K      H
   0.327    0.139    0.420 

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: 546
Number of extensions: 37
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: 458
Length of database: 482
Length adjustment: 33
Effective length of query: 425
Effective length of database: 449
Effective search space:   190825
Effective search space used:   190825
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 24 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:

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