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

GapMind for catabolism of small carbon sources

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

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate Pf6N2E2_3337 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::Q1LZ59
         (655 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337
          Length = 575

 Score =  340 bits (873), Expect = 8e-98
 Identities = 206/526 (39%), Positives = 305/526 (57%), Gaps = 56/526 (10%)

Query: 133 LRQVTNPDDVINLFNATEEEKKEATPAAPVADSHDFLVAVTACTTGIAHTYMAEEALKKQ 192
           LR+     +V    +  E+    +T  AP       LVA+TAC TG+AHT+MA EAL++ 
Sbjct: 88  LRRGAEEAEVFLASDVVEQAPAVSTDRAPR------LVAITACPTGVAHTFMAAEALQQA 141

Query: 193 AAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGI 252
           A ++G  ++VET G+ G  N L+A+ I  A  V++A D  V  +RF GK +        +
Sbjct: 142 ATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLLATDIEVATERFAGKKIYRCSTGIAL 201

Query: 253 KKPEELIN-IILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGG 311
           K+ E  +N  +++G+ E+     S  +S  + SEK G+    YKHL++GVS MLP V+ G
Sbjct: 202 KQAEATLNKALVEGRQESA----SSGASAPAKSEKTGV----YKHLLTGVSFMLPMVVAG 253

Query: 312 GIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEK 371
           G+MIALSF+          +L+        AA+    G+ AF  M+P+ A YIAYSIA++
Sbjct: 254 GLMIALSFVFGIEAFKEPGTLA--------AALMQIGGDTAFKLMVPLLAGYIAYSIADR 305

Query: 372 PGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVL 431
           PGL  G + G +A+T                       + +GF+G +  GFLAG     +
Sbjct: 306 PGLAPGMIGGMLAST-----------------------LGAGFIGGIIAGFLAGYAAKAI 342

Query: 432 KKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLF-VNIPMAAINTALYNFLGNLSGGSAV 490
            +  A +P+SLE +K IL+ PLL  L TG +M++ V  P+A +  AL +FL ++   +A+
Sbjct: 343 SR-YARLPQSLEALKPILIIPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTNAI 401

Query: 491 LLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVA 550
           LLG+++G MM +D+GGP NKAAY F    L + + A      MA+ MA GMVPP+ + +A
Sbjct: 402 LLGVLLGAMMCVDLGGPINKAAYAFSVGLLASQSYAP-----MAATMAAGMVPPIGLGIA 456

Query: 551 TLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLS 610
           T + + KF Q E +AG   +V+GL FI+EGAIPF A DP R IP+ I G A+TGAL    
Sbjct: 457 TFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYF 516

Query: 611 GIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIAGILFGSLRK 653
           G KLMAPHGG+FV+ +    ++ LLYLL I  G+++ G+ +  L++
Sbjct: 517 GCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTGVAYALLKR 562



 Score = 44.3 bits (103), Expect = 2e-08
 Identities = 31/110 (28%), Positives = 53/110 (48%), Gaps = 3/110 (2%)

Query: 172 VTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADK 231
           VTAC  G+  + +    L   A   G    VE + A+    +L+A  ++ A+ V++ A  
Sbjct: 1   VTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLLVASG 60

Query: 232 AVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEA 281
            V+M RF GK L     A  +   +++ +++  G  EA V   SD+  +A
Sbjct: 61  PVDMSRFVGKRLFRSTPALAL---QDVDSVLRRGAEEAEVFLASDVVEQA 107


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: 832
Number of extensions: 40
Number of successful extensions: 7
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: 575
Length adjustment: 37
Effective length of query: 618
Effective length of database: 538
Effective search space:   332484
Effective search space used:   332484
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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Protein sequences (fasta format)
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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
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