GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC

Query= TCDB::Q1LZ59
         (655 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05475
          Length = 579

 Score =  334 bits (856), Expect = 8e-96
 Identities = 209/544 (38%), Positives = 310/544 (56%), Gaps = 54/544 (9%)

Query: 119 ELSQYLLKDGFADKLRQVTNPDDVINLFNATEEEKKEATPA----APVADSHDFLVAVTA 174
           ++S+++ K  F     Q     D +    A E +   A  A    A V+ +   LVAVTA
Sbjct: 68  DMSRFVGKRVFQSTPSQALQDVDAVLRRGAEEAQIYVAPQAVVEPATVSKTAPRLVAVTA 127

Query: 175 CTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAVE 234
           C TG+AHT+MA EAL++ A  +G  ++VET G+ G  N L+A  I  A  V++AAD  V 
Sbjct: 128 CPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAQAIADADVVLLAADIEVA 187

Query: 235 MDRFNGKPLISRPVAEGIKKPEELINIIL-DGKAEAYVADNSDLSSEASSSEKAGLGSAF 293
            +RF GK +        +K+ E  +N  L +GK E     +S +   A   EK G+    
Sbjct: 188 TERFAGKKIYRCGTGIALKQAEATLNKALAEGKQETA---SSGVQGPAKK-EKTGV---- 239

Query: 294 YKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAF 353
           YKHL++GVS MLP V+ GG+MIALSF+          +L+        AA+    G+ AF
Sbjct: 240 YKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEPGTLA--------AALMQIGGDTAF 291

Query: 354 GFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSG 413
             M+P+ A YIAYSIA++PGL  G + G +A+T                       + +G
Sbjct: 292 KLMVPLLAGYIAYSIADRPGLAPGMIGGLLAST-----------------------LGAG 328

Query: 414 FLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-NIPMAA 472
           F+G +  GF+AG     + +  A +P+SLE +K IL+ PLL  L TG +M++V   P+A 
Sbjct: 329 FIGGIIAGFIAGYAAQAINR-YARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAG 387

Query: 473 INTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVV 532
           +  +L +FL ++   +A+LLG+++GGMM +D+GGP NKAAY F    L + + A      
Sbjct: 388 LLESLTHFLDSMGTTNAILLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAP----- 442

Query: 533 MASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARA 592
           MA+ MA GMVPP+ + +AT + + KF Q E +AG   +V+GL FI+EGAIPF A DP R 
Sbjct: 443 MAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRV 502

Query: 593 IPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIAGILFG 649
           IP+ I G A+ GAL    G KLMAPHGG+FV+ +    ++ LLYLL I  G+++  +++ 
Sbjct: 503 IPASIAGGALAGALSMYFGCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYA 562

Query: 650 SLRK 653
           ++++
Sbjct: 563 AVKR 566



 Score = 41.2 bits (95), Expect = 1e-07
 Identities = 26/104 (25%), Positives = 51/104 (49%), Gaps = 1/104 (0%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228
           L  VTAC  G+  + +    L   A   G    VE + A+    +L+A  ++ A+ V++ 
Sbjct: 3   LAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEDAEWVLLV 62

Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVA 272
           +   V+M RF GK +     ++ ++  + ++    + +A+ YVA
Sbjct: 63  STGTVDMSRFVGKRVFQSTPSQALQDVDAVLRRGAE-EAQIYVA 105


Lambda     K      H
   0.320    0.137    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: 825
Number of extensions: 37
Number of successful extensions: 8
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: 655
Length of database: 579
Length adjustment: 37
Effective length of query: 618
Effective length of database: 542
Effective search space:   334956
Effective search space used:   334956
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: 53 (25.0 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