GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1243 ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243
          Length = 521

 Score =  259 bits (662), Expect = 2e-73
 Identities = 161/482 (33%), Positives = 256/482 (53%), Gaps = 15/482 (3%)

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

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
           ++G+ V   +P++A   GI  VFQ  S+ + LSVA+NI +      G     +   RE  
Sbjct: 72  WQGQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTPKQLEPKIRE-- 129

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             + + +G+ ++PE  +   SI  +Q VEI R + +  ++LILDEPTS LT +E ++LF 
Sbjct: 130 --VSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 187

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

Query: 243 EKFYIKEAHEPGEVVLEVKNLS-------GERFENVSFSLRRGEILGFAGLVGAGRTELM 295
           E           +  L V  LS       G   +N+ F +R GEI+G AG+ G G+ EL+
Sbjct: 248 ELITDYPKVMGADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGVAGNGQDELL 307

Query: 296 ETIFG---FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
             + G           I   G+ V    P    + G+  VP +R   G +  +S+  N  
Sbjct: 308 ALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLADNAL 367

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

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           +PK+L+   PT G+DVGA A I+R +  L   G  +++IS +L E+ Q+ DR+  +  G+
Sbjct: 428 QPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRLGALCGGQ 487

Query: 472 LA 473
           L+
Sbjct: 488 LS 489



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 62/222 (27%), Positives = 105/222 (47%), Gaps = 9/222 (4%)

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

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V +      L   +S+  N++L        G      ++ E     +         P+R
Sbjct: 92  MVFQH---FSLFETLSVAQNIALAM------GAAAGTPKQLEPKIREVSQRYGMALEPER 142

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

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           S +L EV  +     V+  G++AG     + S  ++ +L  G
Sbjct: 203 SHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQLMVG 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: 601
Number of extensions: 26
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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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