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

GapMind for catabolism of small carbon sources

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

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  358 bits (919), Expect = e-103
 Identities = 185/483 (38%), Positives = 300/483 (62%), Gaps = 6/483 (1%)

Query: 4   STTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIY 63
           S  P   +  L ++ I K+FPGVKAL +V+L + P  + AL+GENGAGKST++K L GIY
Sbjct: 11  SEDPPVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIY 70

Query: 64  QKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMF--V 121
           Q D G IL  G+ + F + + A ++G++ +HQE  L  + SV +N++LG  P +G F  +
Sbjct: 71  QPDGGRILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAP-RGAFGLI 129

Query: 122 DQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
           D  K     +A+   +  ++DP  ++  L ++   ++ IA+A S  A++VIMDEPT++L+
Sbjct: 130 DWKKTTENARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALS 189

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241
            KE+  L+ ++  LK +G  I++ISHK +EIF++ D  TV RDGQ I    +A +T   +
Sbjct: 190 HKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADL 249

Query: 242 IAMMVGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAK 301
           + MMVGR ++Q FP +    G+ +L V+           D+SF L +GEILG  GLVGA 
Sbjct: 250 VKMMVGRDVSQIFPQRAPNVGDTVLTVQGYA--HPTEFDDISFTLREGEILGFYGLVGAG 307

Query: 302 RTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFN 361
           R++ +++LFGI   SAG++ + G +    +  +A++HG   V E+R   G    L I  N
Sbjct: 308 RSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQN 367

Query: 362 SLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421
             + ++     K G L  +   +  +   + + ++     T +G+LSGGNQQKV+I +WL
Sbjct: 368 VTLPSLGRISRK-GFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWL 426

Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481
            T+P +++LDEPT+G+D+G+K  ++  +AELA +G  +I++SSE+PE+LG++DR++VM  
Sbjct: 427 ATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMRE 486

Query: 482 GLV 484
           G +
Sbjct: 487 GRI 489



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 54/225 (24%), Positives = 109/225 (48%), Gaps = 8/225 (3%)

Query: 278 SIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAIN 337
           ++ DVS  L+ G++  + G  GA ++ +V+ L GI +   G I + G+ +       A +
Sbjct: 35  ALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFSTPQAAAD 94

Query: 338 HGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKT 397
           HG   + +E   T ++  L +  N  + +    +   GL+D  +   + + ++ S+  + 
Sbjct: 95  HGVTAIHQE---TVLFDELSVAENIFLGHAP--RGAFGLIDWKKTTENARALLTSIGAEL 149

Query: 398 -PGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKG 456
            P H+ +   L   N+  V I R L  +  ++++DEPT  +      E+Y+L+  L  +G
Sbjct: 150 DPDHKLK--DLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLKAQG 207

Query: 457 KGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
           K I+ IS +  E+  I D   V  +G + G       T+ +++++
Sbjct: 208 KAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKM 252



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 57/231 (24%), Positives = 109/231 (47%), Gaps = 14/231 (6%)

Query: 7   PSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           P+ G+ +L + G    +      D+++  +R   I    G  GAG+S  ++ LFGI +  
Sbjct: 267 PNVGDTVLTVQG----YAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPS 322

Query: 67  SGTILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWL---GRYPTKGMF 120
           +G++   G   +  S  +A+++GI  V ++      +L   +  N+ L   GR   KG  
Sbjct: 323 AGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFL 382

Query: 121 --VDQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178
              ++  + RE     D     +D    VG LS    Q + IAK  +   +++I+DEPT 
Sbjct: 383 RLAEEFALAREYTERLDLRAASLD--THVGNLSGGNQQKVVIAKWLATRPRVIILDEPTK 440

Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIA 229
            +       +   + +L  +G  ++ +S ++ E+  + D V V+R+G+ +A
Sbjct: 441 GVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVA 491


Lambda     K      H
   0.318    0.136    0.384 

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: 595
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 506
Length of database: 510
Length adjustment: 34
Effective length of query: 472
Effective length of database: 476
Effective search space:   224672
Effective search space used:   224672
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources