GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Dinoroseobacter shibae DFL-12

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  438 bits (1126), Expect = e-127
 Identities = 232/492 (47%), Positives = 332/492 (67%), Gaps = 5/492 (1%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           L +  I K FPGV AL  VS+  YPG+V A++GENGAGKST++KI+ G+YQPD G I+ +
Sbjct: 21  LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF--IDYKKMYREAE 122
           G+ V ++ P  A + G+  + QE  + D LSVAENIF+G    RG F  ID+KK    A 
Sbjct: 81  GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLG-HAPRGAFGLIDWKKTTENAR 139

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             +    G E+DP+ KL    IA + +V IARA+  +A+V+I+DEPT++L+ KE E+L+E
Sbjct: 140 ALL-TSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYE 198

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           +V+SLK +G AI+FISH+ +EIF I D  +V RDG+ IG  +I ++T+  +V+MMVGR +
Sbjct: 199 LVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDV 258

Query: 243 EKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301
            + + + A   G+ VL V+  +    F+++SF+LR GEILGF GLVGAGR+E M+++FG 
Sbjct: 259 SQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGI 318

Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361
                G + I G R EI+ P DA++ GI  VPEDR K G IL + I  NV+LPSL RI +
Sbjct: 319 TRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISR 378

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
             F+    E  LA    +  D+R A  D  V  LSGGNQQKVV+AKWLA +P+++ILDEP
Sbjct: 379 KGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEP 438

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           T+G+D+G+KA ++  M++LA +G+ VIM+SSE+PEVL MSDR+ VM  G++   +   + 
Sbjct: 439 TKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDL 498

Query: 482 SQEKVMKLAAGL 493
             E +++ AAG+
Sbjct: 499 QPETLVRHAAGI 510


Lambda     K      H
   0.318    0.138    0.385 

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: 622
Number of extensions: 32
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 494
Length of database: 510
Length adjustment: 34
Effective length of query: 460
Effective length of database: 476
Effective search space:   218960
Effective search space used:   218960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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