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 GFF2144 PS417_10935 xylose transporter

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__WCS417:GFF2144
          Length = 518

 Score =  400 bits (1028), Expect = e-116
 Identities = 221/499 (44%), Positives = 326/499 (65%), Gaps = 12/499 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD--EGEI 61
           +L++  I K F GV+AL G+ +   PGE   + GENGAGKSTLMK+++ VY     EGEI
Sbjct: 8   LLQMNGIVKSFGGVNALNGIDIRVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWEGEI 67

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMYRE 120
           +++G+ ++    SE   AGIV + QEL+++ +LSVAENIFMG E    G  ++Y  M+  
Sbjct: 68  LWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMFHR 127

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           AE  M+E    +++    + +Y    QQ+VEIA+A+ K+A++LILDEP+S+LT+ E E L
Sbjct: 128 AEALMRELKVPDMNVALPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 187

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
            ++++ LK KGVA ++ISH+L+E+  +CD ++V+RDG++I T ++ ++   KI+  MVGR
Sbjct: 188 LDIIRGLKAKGVACVYISHKLDEVAAVCDTIAVIRDGKHIATTAMADMDIAKIITQMVGR 247

Query: 241 KLEKFYIKEAHEPGEVVLEVKNLS--------GERFENVSFSLRRGEILGFAGLVGAGRT 292
           ++   Y  E H  GEV+ E +N++         +R ++VSF L+RGEILG AGLVGAGRT
Sbjct: 248 EMSNLYPTEPHAVGEVIFEARNVTCHDVDNPKRKRVDDVSFVLKRGEILGIAGLVGAGRT 307

Query: 293 ELMETIFGFRPKR-GGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV 351
           EL+  +FG  P R   E++++G+ ++   PL +I  G+ +VPEDRK+ G+I  + +  N+
Sbjct: 308 ELVSALFGAYPGRYSAEVWLDGQVIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQNI 367

Query: 352 SLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411
           +L  LD       I  + E    D  I    ++ A     +  LSGGNQQK VLAK L  
Sbjct: 368 TLTVLDSYAHRTRIDAEAELGSIDQQIARMHLKTASTFLPITSLSGGNQQKAVLAKMLMA 427

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           KPK+LILDEPTRG+DVGAK EIY++M  LA EGV +IM+SSEL EVL +SDR+ V+  G+
Sbjct: 428 KPKVLILDEPTRGVDVGAKYEIYKLMGALAAEGVAIIMVSSELAEVLGVSDRVLVIGDGQ 487

Query: 472 LAGIIDAKEASQEKVMKLA 490
           L G    +  +QE+V+  A
Sbjct: 488 LRGDFINEGLTQEQVLAAA 506



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 65/242 (26%), Positives = 110/242 (45%), Gaps = 15/242 (6%)

Query: 260 VKNLSGERFEN-VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRG--GEIYIEGKRV 316
           VK+  G    N +   +R GE +G  G  GAG++ LM+ +    P     GEI  +G+ +
Sbjct: 15  VKSFGGVNALNGIDIRVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWEGEILWDGQPL 74

Query: 317 EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKG----PFISFKREKE 372
           +     +    GI ++ ++   L L+  +S+  N+ +     +  G    P +  + E  
Sbjct: 75  KAQSISETEAAGIVIIHQE---LTLVPDLSVAENIFMGHELTLPGGRMNYPAMFHRAEAL 131

Query: 373 LADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAE 432
           + +  +K  D+  A P   V    GG QQ V +AK L  + ++LILDEP+  +       
Sbjct: 132 MRE--LKVPDMNVALP---VSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEV 186

Query: 433 IYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           +  I+  L  +GV  + IS +L EV  + D IAV+  GK        +    K++    G
Sbjct: 187 LLDIIRGLKAKGVACVYISHKLDEVAAVCDTIAVIRDGKHIATTAMADMDIAKIITQMVG 246

Query: 493 LE 494
            E
Sbjct: 247 RE 248


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: 674
Number of extensions: 34
Number of successful extensions: 8
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: 518
Length adjustment: 34
Effective length of query: 460
Effective length of database: 484
Effective search space:   222640
Effective search space used:   222640
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