GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Pseudomonas fluorescens FW300-N2E2

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  319 bits (817), Expect = 2e-91
 Identities = 193/474 (40%), Positives = 284/474 (59%), Gaps = 18/474 (3%)

Query: 37  LCGGNGAGKSTFLSILMGITQRDAG--SILLNGAPV-QFNRPSEALAAGIAMITQELEPI 93
           L G NGAGKST L IL G    DAG  S+  NG  + + + P      GI  I QE   I
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 94  PYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDVDATSPMHRLSVAQIQLVE 153
             M+VAEN++LGREP R G  VD K +    + +LD L   +   + + +LSVA+ Q+VE
Sbjct: 61  ADMSVAENMYLGREPLRHG-FVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVE 119

Query: 154 IAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDY 213
           IAKA + + +++IMDEPT+A+   E   L + I  L A+G  I+YVSH+L+E+    D Y
Sbjct: 120 IAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRY 179

Query: 214 SIFRDGAFVESGRMADIDRDHLVRGIVGQELTRIDHKVGRECAANTCLQVDNLSR----- 268
           +IFRDGA++ SG + D+  D +VR +VG+++  +  K          L+V ++SR     
Sbjct: 180 TIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFV-RKPLTGAPGEVMLKVQSVSRTAAGG 238

Query: 269 -----AGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPM-PI 322
                A    D+S+ +R GEI+G  GL+G+GR+E    I+G    D G + + G+ + P 
Sbjct: 239 GRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPF 298

Query: 323 GLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSL-INARKETQLAEDM 381
             P+  I AG++LV EDRK     L+ SI  N++L +   L  W + I+ R ETQL +D 
Sbjct: 299 KSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDY 358

Query: 382 VKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLL 441
            KRL+IK ++  + + ++SGGNQQKV+LA+C++ +P  L+ DEPTRGID GAK E++ LL
Sbjct: 359 QKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLL 418

Query: 442 DQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLV-TISTDTALSQEALLRLA 494
               R G A IV+SSE PE++ +SDRI  F+ G++   +S D A  +  + R+A
Sbjct: 419 FDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMA 472



 Score = 69.7 bits (169), Expect = 2e-16
 Identities = 55/228 (24%), Positives = 102/228 (44%), Gaps = 13/228 (5%)

Query: 5   LLLQAEHVAKAYAG------VPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQR 58
           ++L+ + V++  AG         L D  + +RAG +    G  GAG++    ++ G    
Sbjct: 224 VMLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGC 283

Query: 59  DAGSILLNGAPVQ-FNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREP-----RRAG 112
           D G I +NG  V  F  P E +AAG+A++ ++ +           W    P     +R G
Sbjct: 284 DEGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWG 343

Query: 113 CIVDNKALNRRTRELLDSLEFDVDATS-PMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPT 171
             +D++A  +  ++    L   +   S  +  LS    Q V +A+  +   +V+I+DEPT
Sbjct: 344 MFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPT 403

Query: 172 SAIGEHEAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDG 219
             I       + + +  +   G  ++ +S  L E+  ++D    FR+G
Sbjct: 404 RGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREG 451


Lambda     K      H
   0.319    0.135    0.381 

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: 599
Number of extensions: 33
Number of successful extensions: 11
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: 495
Length of database: 485
Length adjustment: 34
Effective length of query: 461
Effective length of database: 451
Effective search space:   207911
Effective search space used:   207911
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.

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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