GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas simiae WCS417

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  467 bits (1202), Expect = e-136
 Identities = 243/493 (49%), Positives = 345/493 (69%), Gaps = 4/493 (0%)

Query: 12  YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTIL 71
           YLLE+  I+K FPGV AL +V L+VRP ++ ALMGENGAGKSTL+K + GIYQ D+G I 
Sbjct: 22  YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81

Query: 72  FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRET 130
            +GK I F +   A + GI+M+HQELNL+   S+ +N+W+GR     +  V+  +M+R T
Sbjct: 82  LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
             +   L I++DP  +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TEKEV HLF+
Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
           II  LK +G GIVYI+HKM E+F + DEV V RDG +I  +    +  D +I+MMVGR L
Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261

Query: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
           +Q FP +E   G+++L VR+LT       +DVSFDLH GEILGIAGL+G+ RT++ ET+F
Sbjct: 262 SQLFPLRETPIGDLLLTVRDLT--LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           GI   S+G ITL GK +   + + AI  GFAL+TE+R+ +G++  L +  N  ++ + +Y
Sbjct: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
               G +    +++  + +   +RVKTP     I +LSGGNQQK ++ RWL+T P +L+L
Sbjct: 380 TGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGIDVGAK EIY+LIA LA +G  +I+ISSE+PE+LG++DR++VM  G + G +D 
Sbjct: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498

Query: 491 KTTTQNEILRLAS 503
              TQ ++++LAS
Sbjct: 499 SEATQEKVMQLAS 511



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 51/223 (22%), Positives = 104/223 (46%), Gaps = 6/223 (2%)

Query: 31  NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGI 90
           +V+  +    I  + G  G+G++ + + +FGI    SG I   GK +       A+E G 
Sbjct: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349

Query: 91  SMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVDQDKMYRETKAIFDELDIDIDPRA 145
           +++ ++  L       SV++NM +   P  T   F+ Q  +    + +  +L +      
Sbjct: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409

Query: 146 R-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVY 204
           + + TLS    Q   +A+    N +++I+DEPT  +       ++ +I  L   G  ++ 
Sbjct: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469

Query: 205 ISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVG 247
           IS ++ E+  + D V V+ +G+ + T   +  T +K++ +  G
Sbjct: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512


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: 638
Number of extensions: 30
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 471
Effective length of database: 482
Effective search space:   227022
Effective search space used:   227022
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