GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas putida KT2440

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  326 bits (835), Expect = 1e-93
 Identities = 184/497 (37%), Positives = 299/497 (60%), Gaps = 7/497 (1%)

Query: 9   SGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSG 68
           + E +L   G+ K++     L  V+L++R   + AL GENGAGKSTL K + G+    +G
Sbjct: 12  ANEVVLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTG 70

Query: 69  SIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQ 128
            + ++G+     S  EA   G+ MV QELNL+   +V +N++L   P++  ++   ++ Q
Sbjct: 71  HMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQ 130

Query: 129 DTKAIFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNH 187
              A    + +D IDP   VG L +   QM+EIA+    +  ++I+DEPT+ LT +EV  
Sbjct: 131 LATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVAL 190

Query: 188 LFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVG 247
           LFT I +L+ RG  IVYISH++EE+ ++   I +LRDG+ +  +P++     +++ +MVG
Sbjct: 191 LFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVG 250

Query: 248 RSLNQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVE 307
           R L +       + G  +L+V  L   R   +R+VSF++  GEI GI+GL+GA RT+++ 
Sbjct: 251 RELGEHIDLGRRQLGAPLLKVDKLC--RGDKVREVSFEVRAGEIFGISGLIGAGRTELLR 308

Query: 308 TLFGIREKSSGTITLHG--KKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365
            ++G     SG I L    + ++  +   A+  G AL+TE+R+  G+     I  N  + 
Sbjct: 309 LIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALG 368

Query: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425
           N+    ++ G+LD+   K+  +  I +MR+++ G +  +G LSGGNQQKV+IGRWL    
Sbjct: 369 NL-GAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDC 427

Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485
           ++L+ DEPTRGIDVGAKF+IY L+AELA++GK ++++SS++ EL+ I DRI V+S G + 
Sbjct: 428 QVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLI 487

Query: 486 GIVDTKTTTQNEILRLA 502
                   +Q+++L  A
Sbjct: 488 DTFARDHWSQDQLLAAA 504


Lambda     K      H
   0.319    0.137    0.388 

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: 567
Number of extensions: 23
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 506
Length of database: 524
Length adjustment: 35
Effective length of query: 471
Effective length of database: 489
Effective search space:   230319
Effective search space used:   230319
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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