Alignments for a candidate for fruI in Kocuria turfanensis HO-9042

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Kocuria turfanensis HO-9042

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate WP_062736417.1 AYX06_RS14815 PTS transporter subunit EIIA

Query= TCDB::Q1LZ59
         (655 letters)



>NCBI__GCF_001580365.1:WP_062736417.1
          Length = 712

 Score =  369 bits (948), Expect = e-106
 Identities = 253/720 (35%), Positives = 373/720 (51%), Gaps = 100/720 (13%)

Query: 3   IQDLLNKDVMLLDLQ-ATTKEAAIDEMVSKLVEQGIVTDFDTFKAGIMNREVQTSTGLGD 61
           + +L+  D++ LD      KE  I ++ + +   G     D   A  + RE +T+TG+  
Sbjct: 1   MSELITPDLVSLDRDLGGDKETVIGQLAALVQRTGRAEQLDGLLADAIARENKTATGIPG 60

Query: 62  GIAMPHSKNKAVKEATVLFAKSNKGVDYEALDGEPVDLFFMIAAPDGANDTHLAALAELS 121
           GIA+PH ++ AV E T++ A+  +GV + A DG P D+ F IAAP+GA+ THL  LA+L+
Sbjct: 61  GIAIPHCRSAAVTEPTLVMARLAEGVPWGAKDG-PADIVFFIAAPEGADQTHLKLLAKLA 119

Query: 122 QYLLKDGFADKLRQVTNP-------DDVINLFNATEE--------------------EKK 154
           + L+K  F   LR   +        DD + L  ATE+                    E +
Sbjct: 120 RSLMKKDFVASLRSARSEQEIVRIVDDALGLSPATEDGAAAGATAGSTAAAAVPASVESR 179

Query: 155 EATPAAPVADSHDF------------------LVAVTACTTGIAHTYMAEEALKKQAAEM 196
             T  AP A +                     +VAVTAC TGIAHTYMA + L   A EM
Sbjct: 180 PGTQDAPPAAAEPARSAPAEHAPDAGAPARRRVVAVTACPTGIAHTYMAADGLTYAAEEM 239

Query: 197 GVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAV-EMDRFNGKPLISRPVAEGIKKP 255
           GV ++VET G++G   KL    I  A  VI A D  V +  RF GKP +  PV  GI +P
Sbjct: 240 GVDLQVETQGSAGF-TKLDPATIAAADAVIFATDVDVRDRSRFAGKPYVVSPVKRGIDEP 298

Query: 256 EELINIIL------DGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLPFVI 309
           + +I   L      + K     A  +D  +EAS   + G G+   K +M+GVS M+PFV 
Sbjct: 299 KVMIEEALANAENPNAKRVQGAAGGAD-EAEASGGRE-GWGTRIRKAVMTGVSYMIPFVA 356

Query: 310 GGGIMIALSFLI----------DQFMGVPKSSLSHLGNY---HEIAAIFNQVGNAAFGFM 356
            GG+++A  F++          D   G   S++ +LG +     I A+  ++GN A   +
Sbjct: 357 AGGLLMAFGFMVAGADIANIADDVLTG---STIWNLGEFTLAQYIGAVLFKMGNLAMSLL 413

Query: 357 IPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLG 416
           +P  A YIAY +A++PG+  GF AG +A                         + +GFLG
Sbjct: 414 VPALAGYIAYGLADRPGIAPGFAAGLVANF-----------------------MGAGFLG 450

Query: 417 ALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVT-GFLMLFVNIPMAAINT 475
            + GG LAG     L  A   +PR L  +  +++ PLL  + + G L+L +  P+A    
Sbjct: 451 GIVGGLLAGLAAYWL--AQPRLPRWLGSLMPVVIIPLLATIFSAGLLLLVLGGPIATFMA 508

Query: 476 ALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAA-ALAKGGSVVMA 534
            L   L  ++G SA+ LG I+G MM  D+GGP NK AY F  + L AA A+      +MA
Sbjct: 509 WLTEVLNGMTGASALALGAILGLMMGADLGGPINKVAYTFAAAGLGAATAVNTAPQEIMA 568

Query: 535 SVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIP 594
           +V+A GMVPPLA+ +A+ + K  FT  E + G    ++G SFI+EGAIPF A DP R +P
Sbjct: 569 AVIAAGMVPPLAMALASTVAKRYFTVAEQENGKAAWLLGASFISEGAIPFAAADPLRVLP 628

Query: 595 SFIVGSAVTGALVGLSGIKLMAPHGGIFVIALTSNPLLYLLYIAVGAVIAGILFGSLRKV 654
           + +VG AV GA+   +G+   APHGG++++ +  NPL++LL + VG V+   +  +L+ V
Sbjct: 629 ASMVGGAVAGAISMATGVTSAAPHGGVWILPVIGNPLMFLLSVVVGTVVTAGIVVALKHV 688


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: 1084
Number of extensions: 62
Number of successful extensions: 10
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: 712
Length adjustment: 39
Effective length of query: 616
Effective length of database: 673
Effective search space:   414568
Effective search space used:   414568
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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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