GapMind for catabolism of small carbon sources

 

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

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 3608576 Dshi_1970 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= TCDB::P74224
         (445 letters)



>FitnessBrowser__Dino:3608576
          Length = 688

 Score =  363 bits (931), Expect = e-104
 Identities = 192/458 (41%), Positives = 289/458 (63%), Gaps = 27/458 (5%)

Query: 11  MFVGALVFLGCGYPVAFSLGGVAI--------------LFAIIGAALGSFDPIFLSAMPQ 56
           MF+  +  L  GYPVA+ L GV +              L+  +   L   D + L A   
Sbjct: 232 MFITFIALLFTGYPVAWVLSGVGVAYCGLAFLFDNDLMLWTGLEGTLTGLDYLTLGATVN 291

Query: 57  RIFGIMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLA 116
           R++  M+N  L+A+P FIF+G ML+ SG+AE+L+ +M  + G  RGGLA+ V ++G +LA
Sbjct: 292 RVYATMSNAVLVALPMFIFMGLMLDESGVAERLMTSMQRLFGKTRGGLAITVTMIGIILA 351

Query: 117 ATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGV 176
           A+TG++ A+VV +G++SLP M++  YS  LA+GV+ ASGTLG +IPPS++L+++ADQ+ +
Sbjct: 352 ASTGIIGASVVLLGVLSLPAMMQQKYSPRLAAGVVSASGTLGILIPPSIMLVIMADQMAL 411

Query: 177 SVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLP 236
           SVGDLF+ ++ PG+++ G + +Y+ +I++LKPD+AP +P   ++   Q ++  +V V LP
Sbjct: 412 SVGDLFMAAVFPGVIIGGLYLVYIFVISYLKPDVAP-VPEGAQSPDWQAVKDVMVAV-LP 469

Query: 237 PLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVM 296
            L LIL VLGSIF GI +PTEA  +G++GA  LA   ++L    L  V  +T   T+ + 
Sbjct: 470 TLGLILAVLGSIFAGICTPTEASGIGALGATLLALGYRKLTLHKLVNVLVSTFNTTAYIF 529

Query: 297 LILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIV 356
            I LG+T FS V R L GD  +  ++A    G  G +   +  +F+LGF +D+ EI  IV
Sbjct: 530 AIFLGATVFSYVLRELGGDALIEHMIAATGLGPNGTILFILFIVFLLGFVLDWIEITLIV 589

Query: 357 LPLFKPVAEALNLD-----------LIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPAS 405
           LPL +P+  AL +D           L+W+ ++V   LQTSFLTPP GFALFYL+GV P  
Sbjct: 590 LPLMRPIVNALGMDIPGFGVLDEPTLVWFVILVAVTLQTSFLTPPVGFALFYLKGVCPPE 649

Query: 406 LTTGQIYRGAVPFIGLQVLVLLLIIIFPALINWLPSLS 443
           +    IY+G +PF+ LQ+  L L+ + PAL  WLPS++
Sbjct: 650 IKLLDIYKGIIPFVLLQLTGLALVFLLPALATWLPSVA 687


Lambda     K      H
   0.331    0.148    0.443 

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: 838
Number of extensions: 35
Number of successful extensions: 6
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: 445
Length of database: 688
Length adjustment: 36
Effective length of query: 409
Effective length of database: 652
Effective search space:   266668
Effective search space used:   266668
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 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