Alignments for a candidate for mglA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudomonas fluorescens GW456-L13

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  257 bits (656), Expect = 8e-73
 Identities = 163/495 (32%), Positives = 265/495 (53%), Gaps = 16/495 (3%)

Query: 14  LEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQ 73
           L++R I K +PG  A D ++L + P  IHAL+GENGAGKSTL+K ++G+   DSG +++Q
Sbjct: 14  LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73

Query: 74  GKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKAI 133
           G+ V   +  +A   GI MV Q  +L    SV  N+ L      G      ++    + +
Sbjct: 74  GQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGT---PKQLEPKIREV 130

Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193
                + ++P   V +LS+ + Q +EI +    + +++I+DEPTS LT +E + LF  +R
Sbjct: 131 SRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLR 190

Query: 194 KLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIA-TQPLEGLDMDKIIAMMVGRSLNQ 252
           +L   GC I++ISHK+ E+  LC   T+LR G+      P E  D  ++  +MVG +   
Sbjct: 191 RLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQ-QLARLMVGEAAEL 249

Query: 253 RFPDKENKPGDVILEVRHLTSLRQP-----SIRDVSFDLHKGEILGIAGLVGAKRTDIVE 307
                +   GD  L+VR L S   P     S+ ++  ++ +GEI+GIAG+ G  + +++ 
Sbjct: 250 IADYPKVTGGDACLDVRGL-SWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDELLA 308

Query: 308 TLFG---IREKSSGTITLHGKKINNHTANEAINH-GFALVTEERRSTGIYAYLDIGFNSL 363
            L G   +   +S TI   GK+   H   +A    G A V  ER   G    L +  N+L
Sbjct: 309 LLSGEALLPRNASATIRF-GKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNAL 367

Query: 364 ISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLT 423
           ++  ++     GL+   ++++  + +I    VKTP  +    SLSGGN QK I+GR +L 
Sbjct: 368 LTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREILQ 427

Query: 424 QPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGL 483
           QP +L+   PT G+DVGA   I++ +  L   G  I++IS ++ EL  I+DR+  +  G 
Sbjct: 428 QPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGR 487

Query: 484 VSGIVDTKTTTQNEI 498
           +S +  T  T  +++
Sbjct: 488 LSALHATVDTRLSDV 502



 Score = 55.5 bits (132), Expect = 5e-12
 Identities = 56/249 (22%), Positives = 106/249 (42%), Gaps = 34/249 (13%)

Query: 266 LEVRHLTSLRQPSIRDVSFDLH--KGEILGIAGLVGAKRTDIVETLFGIREKSSGTITLH 323
           L++R +T      + + + DL    GEI  + G  GA ++ +++ ++G+    SG +   
Sbjct: 14  LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73

Query: 324 GKKINNHTANEAINHGFALVTE-----ERRSTGIYAYLDIGF-----NSLISNIRNYKNK 373
           G++++     +A   G  +V +     E  S      L +G        L   IR    +
Sbjct: 74  GQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTPKQLEPKIREVSRR 133

Query: 374 VGL-LDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDE 432
            G+ L+  R+                     + SLS G +Q+V I R L+    +L+LDE
Sbjct: 134 YGMTLEPERL---------------------VHSLSIGERQRVEIIRCLMQDIRLLILDE 172

Query: 433 PTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKT 492
           PT  +      +++  +  LA +G  I+ IS ++ E+  +     V+  G V+G      
Sbjct: 173 PTSVLTPQEADDLFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAE 232

Query: 493 TTQNEILRL 501
            +  ++ RL
Sbjct: 233 CSDQQLARL 241



 Score = 49.7 bits (117), Expect = 3e-10
 Identities = 54/251 (21%), Positives = 105/251 (41%), Gaps = 12/251 (4%)

Query: 10  GEYLLEMRGINKSFPGVK--ALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFG--IYQK 65
           G+  L++RG++   P     +L N++L VR   I  + G  G G+  LL  L G  +  +
Sbjct: 259 GDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDELLALLSGEALLPR 318

Query: 66  DSGSIVFQGKEVDFHSAKEALEN-GISMVHQEL---NLVLQRSVMDNMWLGRYP---TKG 118
           ++ + +  GKE   H   +A    G++ V  E      V + S+ DN  L  +       
Sbjct: 319 NASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNALLTAFQHGLVSN 378

Query: 119 MFVDQDKMYQDTKAIFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPT 177
             + + K+    + I     +   D +A   +LS   +Q   + +      ++++   PT
Sbjct: 379 GLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREILQQPRLLVAAHPT 438

Query: 178 SSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLD 237
             +       +   +  L++ G  I+ IS  ++E+FQ+ D +  L  G+  A        
Sbjct: 439 WGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGRLSALHATVDTR 498

Query: 238 MDKIIAMMVGR 248
           +  +   M G+
Sbjct: 499 LSDVGGWMAGQ 509


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: 557
Number of extensions: 31
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: 521
Length adjustment: 35
Effective length of query: 471
Effective length of database: 486
Effective search space:   228906
Effective search space used:   228906
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:

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
the source code
instructions for running GapMind on your computer

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