GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Pseudomonas simiae WCS417

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate GFF2144 PS417_10935 xylose transporter

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__WCS417:GFF2144
          Length = 518

 Score =  348 bits (893), Expect = e-100
 Identities = 203/500 (40%), Positives = 303/500 (60%), Gaps = 12/500 (2%)

Query: 20  ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN--EGEI 77
           +L+M GI + F GV AL+ + I + PG    L GENGAGKSTL+K+L+ +Y     EGEI
Sbjct: 8   LLQMNGIVKSFGGVNALNGIDIRVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWEGEI 67

Query: 78  LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137
           L DG+P    S      AG+  IHQE  L  +L+VAENIF+GH        +++  M  R
Sbjct: 68  LWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMFHR 127

Query: 138 SKALLTALE-SNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDL 196
           ++AL+  L+  +++  + +       + LV IA+AL+ +AR++I+DEP++AL+R EI+ L
Sbjct: 128 AEALMRELKVPDMNVALPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 187

Query: 197 FRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVG 256
             I+RGLK +G A ++ISHK DE+  + D   V  R  +             +I+  MVG
Sbjct: 188 LDIIRGLKAKGVACVYISHKLDEVAAVCDTIAVI-RDGKHIATTAMADMDIAKIITQMVG 246

Query: 257 RDVENVFPKIDVAIGGPVLEIRNYS-------HRTEFRDISFTLRKGEILGVYGLIGAGR 309
           R++ N++P    A+G  + E RN +        R    D+SF L++GEILG+ GL+GAGR
Sbjct: 247 REMSNLYPTEPHAVGEVIFEARNVTCHDVDNPKRKRVDDVSFVLKRGEILGIAGLVGAGR 306

Query: 310 SELSQSLFGITKP-LSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQN 368
           +EL  +LFG      S ++ L+GQ I   +P  +IRAG+  VPE+R R G+   + + QN
Sbjct: 307 TELVSALFGAYPGRYSAEVWLDGQVIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQN 366

Query: 369 MTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428
           +TL  L   + R  + A  E     +   R+ L+ A+  +P+ +LSGGNQQK V+ K L 
Sbjct: 367 ITLTVLDSYAHRTRIDAEAELGSIDQQIARMHLKTASTFLPITSLSGGNQQKAVLAKMLM 426

Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEG 488
             PKV+ILDEPT+G+D+G+K  ++  +  LAAEG++IIMVSSEL E++G+SDRVLV+ +G
Sbjct: 427 AKPKVLILDEPTRGVDVGAKYEIYKLMGALAAEGVAIIMVSSELAEVLGVSDRVLVIGDG 486

Query: 489 LSAGIFERAELSPEALVRAA 508
              G F    L+ E ++ AA
Sbjct: 487 QLRGDFINEGLTQEQVLAAA 506



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 58/239 (24%), Positives = 106/239 (44%), Gaps = 12/239 (5%)

Query: 277 IRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITK--PLSGKMVLEGQEI 334
           ++++        I   +R GE +G+ G  GAG+S L + L  +       G+++ +GQ +
Sbjct: 15  VKSFGGVNALNGIDIRVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWEGEILWDGQPL 74

Query: 335 TIHSPQDAIRAGIVYVPEERGR-HGLALPMPIFQN--MTLPSLARTSRRGFLRAANEFAL 391
              S  +   AGIV + +E      L++   IF    +TLP        G +     F  
Sbjct: 75  KAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPG-------GRMNYPAMFHR 127

Query: 392 ARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAV 451
           A      L +    +++PV    GG QQ V I K L    +++ILDEP+  +       +
Sbjct: 128 AEALMRELKVPDMNVALPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 187

Query: 452 HGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
              I  L A+G++ + +S +L E+  + D + V+++G        A++    ++    G
Sbjct: 188 LDIIRGLKAKGVACVYISHKLDEVAAVCDTIAVIRDGKHIATTAMADMDIAKIITQMVG 246


Lambda     K      H
   0.320    0.137    0.382 

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: 586
Number of extensions: 26
Number of successful extensions: 10
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: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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