Alignments for a candidate for fruI in Collinsella tanakaei YIT 12063

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Collinsella tanakaei YIT 12063

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_009140199.1 HMPREF9452_RS00845 PTS transporter subunit EIIA

Query= TCDB::Q1LZ59
         (655 letters)



>NCBI__GCF_000225705.1:WP_009140199.1
          Length = 684

 Score =  371 bits (952), Expect = e-107
 Identities = 216/501 (43%), Positives = 302/501 (60%), Gaps = 23/501 (4%)

Query: 162 VADSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKR 221
           +A+ +D ++A T C TGIAHT+MA+EAL+K AAE G+ IKVET+G  G+ N LT  +I  
Sbjct: 1   MAEKYD-IIAATGCPTGIAHTFMAKEALEKAAAERGLTIKVETHGQVGIENALTPAEIAA 59

Query: 222 AKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKPE--ELINIILDGKAEAYVADNSDLSS 279
           A+ V++AADK V  +RF GKP++S  V+  I +     LI+  L  KA+      + ++ 
Sbjct: 60  ARAVVVAADKDVNAERFAGKPMVSVGVSRAISQEAAGRLIDDALAAKADPNAV--AAVAQ 117

Query: 280 EASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYH 339
           EA S+EK   G   YKHLM+GVS ML FV+ GG++ A+SFL     G+     S   +Y+
Sbjct: 118 EALSAEKESFGHQLYKHLMNGVSHMLVFVVAGGVLTAVSFL----WGITSFD-STASDYN 172

Query: 340 EIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFG 399
             AA+   +G  A   M+PV +AYIA SI ++P LV GFVAG +A  GL  +     E G
Sbjct: 173 TFAAMLKTIGGIAMNLMVPVLSAYIAESIGKRPALVPGFVAGMIAIQGLPVSA----ETG 228

Query: 400 EKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVT 459
                A  +G+  GFLG + GGFL+G VIL+L+K  A +P +L G+K+I LYPL   L+ 
Sbjct: 229 --LIDAGGSGVGFGFLGGIVGGFLSGYVILLLEKIFAKLPANLNGLKAIFLYPLFSTLIV 286

Query: 460 GFLMLFVNIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTST 519
           G +ML ++ PM  IN  + +FL +L    A+ LG+ +G M A+DMGGP NKAAYV GT  
Sbjct: 287 GLVMLGISGPMVTINNGMMDFLRSLQHAGAIPLGIAIGCMCAVDMGGPVNKAAYVTGTML 346

Query: 520 LTAAALA-------KGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVM 572
           L     A         G+  MA+V A  +VPPL    A +  K  F+QE+HDAG+ NI++
Sbjct: 347 LGVGLEAGVGTSEYADGTAFMAAVSAACIVPPLVTSFAVIAGKKYFSQEDHDAGIVNIIL 406

Query: 573 GLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIALTSNPLL 632
           G + ITEGAIPF   +    +P  +V SA+   L  L G+ + APHGG  V+ +    L 
Sbjct: 407 GCTHITEGAIPFMTKNIWPVMPIMMVSSAIASVLTLLLGVHVPAPHGGFLVLPVVDGGLQ 466

Query: 633 YLLYIAVGAVIAGILFGSLRK 653
           ++L I VG V+ GILF + +K
Sbjct: 467 WVLAILVGTVVGGILFTAFKK 487



 Score = 76.3 bits (186), Expect = 4e-18
 Identities = 43/135 (31%), Positives = 72/135 (53%), Gaps = 2/135 (1%)

Query: 15  DLQATTKEAAIDEMVSKLVEQGIVTDFDTFKAGIMNREVQTSTGLGDGIAMPHSKNKAVK 74
           D +   ++AA+  +    V  GI  D D   A  + RE + +TG+ DG A+PH+K  AVK
Sbjct: 546 DQKVDDRDAALKFISDNAVAAGIADDADALLAAFLKREAEGTTGMVDGFAIPHAKTDAVK 605

Query: 75  EATVLFAKSNKGV-DYEALDGEPVDLFFMIAAPDG-ANDTHLAALAELSQYLLKDGFADK 132
           +A+V+  K+ +GV  ++ +D  PV     +  P+  A  +HL  L++++  L  D F   
Sbjct: 606 QASVMVLKAPEGVPGWDTMDEAPVTCAIALLVPEAEAGTSHLQILSKVAMALTDDDFRAA 665

Query: 133 LRQVTNPDDVINLFN 147
            +  T+P  V +L N
Sbjct: 666 CKDATDPAAVASLIN 680


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: 1034
Number of extensions: 51
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: 684
Length adjustment: 39
Effective length of query: 616
Effective length of database: 645
Effective search space:   397320
Effective search space used:   397320
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 2024 update 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