Aligments for a candidate for mglA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for mglA in Phaeobacter inhibens BS107

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__Phaeo:GFF385 PGA1_c03960 ribose import
           ATP-binding protein RbsA
          Length = 509

 Score =  285 bits (728), Expect = 4e-81
 Identities = 165/498 (33%), Positives = 286/498 (57%), Gaps = 19/498 (3%)

Query: 14  LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73
           +E+ GI+K+F  V+A  +++++V P +IH ++GENGAGKSTL+  L+G Y+ D G +   
Sbjct: 6   IELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIH 65

Query: 74  GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133
           GK  +   ++ A+  GI MV Q   LV   +V++N+ LG      +     K  +  K +
Sbjct: 66  GKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKARKSLKDL 125

Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193
             E ++++DP AR+  + V   Q +EI KA    A I+I+DEPT  LT  E + LF I+ 
Sbjct: 126 AAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILD 185

Query: 194 KLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQR 253
           +L+  G  I+ I+HK+ EI +  D V+V+R G+  AT   A  + + +  +MVGR +  R
Sbjct: 186 RLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKVLLR 245

Query: 254 FPDKENKPGEVILEVRNLTSLRQPS---IRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
                  PG+ ILE+ NL+ + +     ++++   +  GEILGIAG+ G  +++++E L 
Sbjct: 246 VDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLG 305

Query: 311 GIREKSAGTITLHGKQI------NNHNANEAINHGFALVTEERRSTGI----YAYLDIGF 360
           G+RE   G+I L+G  +      ++  A  A +   A V E+R+  G+    +A+ ++ F
Sbjct: 306 GMRE-GQGSIRLNGAPLPLSGAGSDARARRAAH--VAHVPEDRQREGLIMDFHAWENVAF 362

Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420
                +   Y+  + L++N+ +++DT+  +    V+ P       + SGGNQQK+++ R 
Sbjct: 363 G--YHHAPEYQRGL-LMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVARE 419

Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480
           +   PE+L++ +PTRG+D+GA   I++ I EL  +GK I+++S E+ E+L + DR+ VM 
Sbjct: 420 IERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMF 479

Query: 481 NGLVSGIVDTKTTTQNEI 498
           +G++ G      T + E+
Sbjct: 480 DGMIMGERPADQTDEKEL 497



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 57/229 (24%), Positives = 107/229 (46%), Gaps = 21/229 (9%)

Query: 280 RDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHG 339
           +D+S  +  G I GI G  GA ++ ++  L+G  +   G + +HGK+    ++  AI+ G
Sbjct: 22  KDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIHGKRTEIPDSQAAISAG 81

Query: 340 FALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKV-GLLDNSRMKSDTQWVIDSMRVKTP 398
             +V +  +              L+ N    +N + G  D   +K        S++    
Sbjct: 82  IGMVFQHFK--------------LVENFTVLENIILGAEDGGLLKPSLSKARKSLKDLAA 127

Query: 399 GHR------TQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAEL 452
            +        +I  +  G QQ+V I + L  Q +IL+LDEPT  +      ++++++  L
Sbjct: 128 EYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILDRL 187

Query: 453 AKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
             +GK II+I+ ++ E++  TD + VM  G ++  V T  T+   +  L
Sbjct: 188 RAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAEL 236



 Score = 68.2 bits (165), Expect = 7e-16
 Identities = 58/258 (22%), Positives = 119/258 (46%), Gaps = 15/258 (5%)

Query: 2   VSSTTPSSGEYLLEMSGINK-SFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF 60
           V     + G+ +LE+  ++     GV  + N++L VR   I  + G  G G+S L++ L 
Sbjct: 246 VDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLG 305

Query: 61  GIYQKDSGTILFQGKEI-------DFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGR 113
           G+ ++  G+I   G  +       D  + + A    +    Q   L++     +N+  G 
Sbjct: 306 GM-REGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGY 364

Query: 114 YPT----KGMFVDQDKMYRETKAIFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNA 168
           +      +G+ ++   +  +T+A   + D+   DP       S    Q I +A+    N 
Sbjct: 365 HHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNP 424

Query: 169 KIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWI 228
           +++++ +PT  +    +  +   I +L+++G  I+ +S ++EEI  L D V V+ DG  +
Sbjct: 425 ELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIM 484

Query: 229 ATEPLAGLTMDKIIAMMV 246
              P A  T +K + +++
Sbjct: 485 GERP-ADQTDEKELGLLM 501


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: 616
Number of extensions: 32
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: 509
Length adjustment: 34
Effective length of query: 472
Effective length of database: 475
Effective search space:   224200
Effective search space used:   224200
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:

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, 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

GapMind for catabolism of small carbon sources