GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rhaT' in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_523 Inositol transport system ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Inositol transport
           system ATP-binding protein
          Length = 517

 Score =  399 bits (1025), Expect = e-115
 Identities = 207/497 (41%), Positives = 322/497 (64%), Gaps = 5/497 (1%)

Query: 16  DAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEG 75
           D P +LE+  +S+ FPGV AL +V + + PG+V AL+GENGAGKSTL+KI+ GIY+P+ G
Sbjct: 22  DEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 81

Query: 76  EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMN 135
           E+ + G+P TF +  AA+ AG+  IHQE  L   +++AENI++G         +D   M+
Sbjct: 82  ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMH 141

Query: 136 SRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDD 195
             +  LL  L   +DP  ++ +LSIA+R +V IA+A+S ++ I+IMDEPT+A++  E+  
Sbjct: 142 RCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAH 201

Query: 196 LFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQD--EIVRM 253
           LF I+  LK QGK I++I+HK +E++ IAD+  VF   +     G+ R    D   ++ M
Sbjct: 202 LFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGA---YIGLQRADSMDGDSLISM 258

Query: 254 MVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELS 313
           MVGR++  +FP  +  IG  VL +R+ S    F+ +SF L  GEILG+ GL+G+GR+ ++
Sbjct: 259 MVGRELSQLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVA 318

Query: 314 QSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPS 373
           +++FG+T    G+++L+GQ + I  P  AI  G   + E+R   GL   + + +NM +  
Sbjct: 319 EAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 378

Query: 374 LARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKV 433
           L      GF++     AL     ++L ++  +L   + TLSGGNQQK ++ +WL T P++
Sbjct: 379 LPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 438

Query: 434 IILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGI 493
           +ILDEPT+GID+G+KA ++  IS LA+EG+++IM+SSELPE++GMSDRV+VM EG   G 
Sbjct: 439 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 498

Query: 494 FERAELSPEALVRAATG 510
             R E + E +++ A+G
Sbjct: 499 LNRGEATQERVMQLASG 515


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: 603
Number of extensions: 40
Number of successful extensions: 7
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: 512
Length of database: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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