Alignments for a candidate for rhaT' in Pseudomonas simiae WCS417

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources