GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas stutzeri RCH2

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__psRCH2:GFF1357
          Length = 518

 Score =  272 bits (696), Expect = 2e-77
 Identities = 172/505 (34%), Positives = 271/505 (53%), Gaps = 17/505 (3%)

Query: 7   PSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           P S    L++ GI K +PG  A D ++L ++P  IHAL+GENGAGKSTL+K ++G+ Q D
Sbjct: 2   PDSQTARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPD 61

Query: 67  SGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKM 126
           +G I +QG+ +      +A E GI MV Q  +L    SV +N+ L      G     +  
Sbjct: 62  AGEIHWQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAGTPKQLEPK 121

Query: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
            RE   +     + ++P+  V +LS+ + Q +EI +    + +++I+DEPTS LT +E +
Sbjct: 122 IRE---VSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEAD 178

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIA-MM 245
            LF  +R+L   GC I++ISHK+ E+  LC   TVLR G+ ++ E +     D  +A +M
Sbjct: 179 ELFVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGR-VSGECIPAECSDLELARLM 237

Query: 246 VG--RSLNQRFPDKENKPGEVILEVRNLTSLRQP----SIRDVSFDLHKGEILGIAGLVG 299
           VG    L   +P  E +     L V  L+         S+++V  ++  GEI+GIAG+ G
Sbjct: 238 VGDAEGLEAEYPKSEGRAP--FLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAG 295

Query: 300 AKRTDIVETLFG---IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYL 356
             + +++  L G   ++   A  I   G  + +        HG A V  ER   G    +
Sbjct: 296 NGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSM 355

Query: 357 DIGFNSLISNIRNYKN-KVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKV 415
            +  N L++  +     + GL+   R+++  + VI    VKTP  +T   SLSGGN QK 
Sbjct: 356 SLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKF 415

Query: 416 IIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDR 475
           I+GR +L QP++L+   PT G+DVGA   I++ + EL   G  I++IS ++ EL  I+DR
Sbjct: 416 ILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDR 475

Query: 476 ILVMSNGLVSGIVDTKTTTQNEILR 500
           I  +S+G +S    T +T   E+ R
Sbjct: 476 IAALSDGRLSPQRATASTCPVEVGR 500



 Score = 60.1 bits (144), Expect = 2e-13
 Identities = 51/221 (23%), Positives = 100/221 (45%), Gaps = 12/221 (5%)

Query: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFA 341
           +   +  GEI  + G  GA ++ +++ ++G+ +  AG I   G+++   +  +A   G  
Sbjct: 27  IDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERVTMRDPAQARERGIG 86

Query: 342 LVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHR 401
           +V +      ++  L +  N  ++        +G    +  + + +    S R   P   
Sbjct: 87  MVFQH---FSLFETLSVAENIALA--------LGAKAGTPKQLEPKIREVSQRYGMPLEP 135

Query: 402 TQ-IGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGII 460
            + + SLS G +Q+V I R L+    +L+LDEPT  +      E++  +  LA +G  I+
Sbjct: 136 QRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSIL 195

Query: 461 IISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
            IS ++ E+  +     V+  G VSG       +  E+ RL
Sbjct: 196 FISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARL 236


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: 563
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: 2
Length of query: 506
Length of database: 518
Length adjustment: 35
Effective length of query: 471
Effective length of database: 483
Effective search space:   227493
Effective search space used:   227493
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