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

GapMind for catabolism of small carbon sources

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

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  270 bits (689), Expect = 1e-76
 Identities = 165/484 (34%), Positives = 259/484 (53%), Gaps = 15/484 (3%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P L+++ I KR+PG  A   + +   PGE+HA++GENGAGKSTLMKII GV   D GE+I
Sbjct: 12  PRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVI 71

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
           ++G+ V   +P++A   GI  VFQ  S+ + LSVA+NI +      G     +   RE  
Sbjct: 72  WQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTPKQLEPKIREVS 131

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           +     +G+ ++PE  +   SI  +Q VEI R + +  ++LILDEPTS LT +E + LF 
Sbjct: 132 R----RYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFV 187

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
            ++ L  +G +I+FISH+L E+  +C   +VLR G   G       + +++  +MVG   
Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGEAA 247

Query: 243 EKFYIKEAHEPGEVVLEVKNLS-------GERFENVSFSLRRGEILGFAGLVGAGRTELM 295
           E          G+  L+V+ LS       G    N+   +RRGEI+G AG+ G G+ EL+
Sbjct: 248 ELIADYPKVTGGDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDELL 307

Query: 296 ETIFG--FRPKRGGEIYIEGKRVEINHPLDAIEQ-GIGLVPEDRKKLGLILIMSIMHNVS 352
             + G    P+        GK    +   DA  Q G+  VP +R   G +  +S+  N  
Sbjct: 308 ALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNAL 367

Query: 353 LPSLDR-IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411
           L +    +     I   + + LA+  I+ F ++          LSGGN QK +L + +  
Sbjct: 368 LTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREILQ 427

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           +P++L+   PT G+DVGA A I+R +  L   G  +++IS +L E+ Q+SDR+  +  G+
Sbjct: 428 QPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGR 487

Query: 472 LAGI 475
           L+ +
Sbjct: 488 LSAL 491



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 62/222 (27%), Positives = 111/222 (50%), Gaps = 9/222 (4%)

Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330
           +  ++  GEI    G  GAG++ LM+ I+G      GE+  +G+RV + +P  A   GIG
Sbjct: 32  IDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIG 91

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V +      L   +S+  N++L ++      P     + +E++     T +     P+R
Sbjct: 92  MVFQH---FSLFETLSVAQNIAL-AMGAAAGTPKQLEPKIREVSRRYGMTLE-----PER 142

Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450
            V  LS G +Q+V + + L    ++LILDEPT  +      +++  + +LA EG  ++ I
Sbjct: 143 LVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSILFI 202

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           S +L EV  +     V+  G++AG     E S +++ +L  G
Sbjct: 203 SHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVG 244


Lambda     K      H
   0.318    0.138    0.385 

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: 589
Number of extensions: 24
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: 494
Length of database: 521
Length adjustment: 34
Effective length of query: 460
Effective length of database: 487
Effective search space:   224020
Effective search space used:   224020
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources