GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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