GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Pseudomonas simiae WCS417

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 GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__WCS417:GFF2673 PS417_13635 D-ribose transporter
           ATP-binding protein
          Length = 510

 Score =  419 bits (1077), Expect = e-121
 Identities = 232/501 (46%), Positives = 335/501 (66%), Gaps = 10/501 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEG- 59
           ++P+LE++ I K F G+  LK V ++ YPGE+HA++GENGAGKSTLMKI++G YQ D G 
Sbjct: 3   LEPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGG 62

Query: 60  EIIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYR 119
           EI   G+ +    P+ A   GI  ++QELS+  NLSVAENI++G E +RG  ID K M  
Sbjct: 63  EIRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEA 122

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
              + + +  G E  P  ++   SIA +Q+VEIARA++  AK+L++DEPT+ L+ +ET++
Sbjct: 123 GCIEVL-QRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDR 181

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           LF ++K L+ +G+AII+ISHR+ EI+ + D+VSVLRDG YIG  + + L+ E +V+MMVG
Sbjct: 182 LFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVG 241

Query: 240 RKLEKFYIKE--AHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           R L  FY KE  A+ PG VV+ V++++ G+R  + SF L  GE+LG AGLVGAGRTEL  
Sbjct: 242 RDLSGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELAR 301

Query: 297 TIFGFRPKRGGEIYIEGKRV-EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL-P 354
            IF   P+  G + + GK V  +  P DAI  G+  + EDRK  GL L MS+  N+++  
Sbjct: 302 LIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINVCA 361

Query: 355 SLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPK 414
            +     G  +      + ++ AIK+  IR A        LSGGNQQKV+LA+ L +KP 
Sbjct: 362 CVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVKPH 421

Query: 415 ILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL-- 472
           +LILDEPTRG+D+G+K+EIYRI++QLA+ G+G+++ISSELPE++   DR+ +M  G+L  
Sbjct: 422 VLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQLVA 481

Query: 473 -AGIIDAKEASQEKVMKLAAG 492
             G    +  SQE+++ LA G
Sbjct: 482 EVGGASGQAISQERIIDLATG 502


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: 679
Number of extensions: 37
Number of successful extensions: 10
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: 494
Length of database: 510
Length adjustment: 34
Effective length of query: 460
Effective length of database: 476
Effective search space:   218960
Effective search space used:   218960
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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