GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Kocuria flava HO-9041

Align The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter

Query= TCDB::Q9XIH7
         (511 letters)



>NCBI__GCF_001482365.1:WP_058858199.1
          Length = 482

 Score =  219 bits (559), Expect = 1e-61
 Identities = 143/459 (31%), Positives = 238/459 (51%), Gaps = 23/459 (5%)

Query: 30  AILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAGRTSDW 89
           +I+A    ++ GYD GV++GA   + ++L L+     ++   L   + VG+ + GR SD 
Sbjct: 30  SIVACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRISDA 89

Query: 90  LGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEVAPASS 149
            GRR TI+L    FF G +++ F  NY  ++ GR   G+ VG A  + PV+ AE+AP   
Sbjct: 90  WGRRRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAPYEI 149

Query: 150 RGFLTSFPEIFINIGILLGYVSNYFFSK--LPEHLGWRFMLGVGAVPSVFLAIGVLAMPE 207
           RG +    E+ I IG L  +V N       +     WR+M  + A+P+V L +G+L MPE
Sbjct: 150 RGSIAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLRMPE 209

Query: 208 SPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIVVPNKKSAGK 267
           SPRWLV +GR  +A +VL ++  ++E A++ L +++               V  ++SA  
Sbjct: 210 SPRWLVEKGRHEEALEVL-RSVRSEERAVAELGEVEH--------------VAEEESAEN 254

Query: 268 GVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLLATV 327
            +    ++R    +R I++  +G+  AQQ +GI++++ Y   +  ++G  S +  L+A +
Sbjct: 255 RIGLGAVLRNKWLIR-IMLVGIGLGIAQQLTGINSIMYYGQIVLIESGF-SASAALIANI 312

Query: 328 AVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNPGQTLKWAIG 387
           A GV+  +   +   ++DR  RR   +            +G +  V+    G  L+  + 
Sbjct: 313 APGVIAVVGGFIALAMMDRLDRRKTFVIGFSLTTTCHLLIGIASVVLEE--GNPLRPFVI 370

Query: 388 LAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMTFLSLS 447
           LA+  V+ FV +         WVY SE+FP+ +R  G  + +    + +G++ + F SL 
Sbjct: 371 LAL--VVAFVGSMQTFLNVAVWVYLSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLV 428

Query: 448 KGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEME 486
             + I G F LFAGV   A VF  T +PETRG  LE +E
Sbjct: 429 DAVGITGTFFLFAGVGVLALVFVATQVPETRGRTLEALE 467


Lambda     K      H
   0.324    0.140    0.415 

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: 657
Number of extensions: 40
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: 511
Length of database: 482
Length adjustment: 34
Effective length of query: 477
Effective length of database: 448
Effective search space:   213696
Effective search space used:   213696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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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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