GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2673
          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 (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