GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Pseudomonas fluorescens FW300-N2E2

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 D-xylose transport
           ATP-binding protein XylG
          Length = 518

 Score =  369 bits (947), Expect = e-106
 Identities = 210/505 (41%), Positives = 314/505 (62%), Gaps = 11/505 (2%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--G 68
           +YLL+M+GI K+F GVKAL+ +++KVRP     L GENGAGKSTL+K L  +Y   +  G
Sbjct: 3   DYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDG 62

Query: 69  TILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMY 127
            IL+ G+ +   S  E    GI ++HQEL LV   SV +N+++G   T  G  ++   M 
Sbjct: 63  EILWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMI 122

Query: 128 RETKAIFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
              +A+  EL + D++    V        Q++EIAKA +  A+++I+DEP+S+LT  E+ 
Sbjct: 123 HRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIE 182

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246
            L  IIR LK +G   VYISHK++E+  +CD ++V+RDG+ IAT  +A +++ KII  MV
Sbjct: 183 VLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMV 242

Query: 247 GRSLNQRFPDKENKPGEVILEVRNLT-----SLRQPSIRDVSFDLHKGEILGIAGLVGAK 301
           GR ++  +P + +  GEVI E R+ T     + R+  + D+SF L +GEILGIAGLVGA 
Sbjct: 243 GREMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAG 302

Query: 302 RTDIVETLFGIRE-KSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF 360
           RT++V  LFG    +  G + L+G+QI+     ++I  G  +V E+R+  GI   L +G 
Sbjct: 303 RTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQ 362

Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420
           N  ++ + NY +K+  +D           I  M +KT      I SLSGGNQQK ++ + 
Sbjct: 363 NITLAVLDNY-SKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLAKM 421

Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480
           LLT+P +L+LDEPTRG+DVGAK+EIY+L+  LA +G  II++SSE+ E+LG++DR+LV+ 
Sbjct: 422 LLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIG 481

Query: 481 NGLVSGIVDTKTTTQNEILRLASLH 505
           +G + G       TQ ++L  A  H
Sbjct: 482 DGQLRGDFINHELTQEQVLAAALSH 506


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: 605
Number of extensions: 27
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: 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 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