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

GapMind for catabolism of small carbon sources

Aligments 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:

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 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

GapMind for catabolism of small carbon sources