Alignments for a candidate for fruII-ABC in Catellicoccus marimammalium M35/04/3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Catellicoccus marimammalium M35/04/3

Align Chromosomal fructose Enzyme IIABC (Fru1) of 654 aas; in an operon with fructose-1-P kinase (characterized)
to candidate WP_009489923.1 C683_RS03175 PTS sugar transporter subunit IIA

Query= TCDB::Q3K0G6
         (654 letters)



>NCBI__GCF_000313915.1:WP_009489923.1
          Length = 632

 Score =  747 bits (1928), Expect = 0.0
 Identities = 391/652 (59%), Positives = 489/652 (75%), Gaps = 24/652 (3%)

Query: 1   MKIQDLLKKEVMIMDLKATSKEAAIDEMITKLVDTGVVTNFAIFKDGIMKREAQTSTGLG 60
           M +  LL ++ MI+DLKAT+K  AIDEM+ +L + GV+ + A FK+GI+KREAQ+STGLG
Sbjct: 1   MDVTKLLNQDCMILDLKATNKADAIDEMVQRLYEAGVIQDVASFKEGILKREAQSSTGLG 60

Query: 61  DGIAMPHSKNAAVKEATVLFAKSASGVDYEALDGQPTDLFFMIAAPDGANDTHLAALAEL 120
           DGIA+PH+K A+VK+ATVLFA+S  G+DYEALDGQ T LFFMIAAP+GAN+ HL AL+ L
Sbjct: 61  DGIAIPHAKCASVKQATVLFARSKQGLDYEALDGQNTHLFFMIAAPEGANNEHLQALSAL 120

Query: 121 SKYLLKEGFADQLRQAKTPDDIIATFDSNSISQETVAPQTVQSTSKGSDYIVAVTACTTG 180
           S+ L+   F  +L++  + + +I  F      +E      V+  +  + +IVAVTAC TG
Sbjct: 121 SQLLMNPSFVGKLKEVTSKEQVIELFKEEQKEEEKQNQPAVEENND-APFIVAVTACPTG 179

Query: 181 IAHTYMAEEALKKKAAEMGVGIKVETNGASGVGNKLTSSDIARAKGVIIAADKAVEMDRF 240
           IAHTYMAE+AL + A ++ V IKVETNG+ G  N LTS +IA+A+ VIIAADK VE  RF
Sbjct: 180 IAHTYMAEKALYQAAKDLNVNIKVETNGSDGAKNVLTSDEIAKAQAVIIAADKKVETARF 239

Query: 241 DGKPLVSRPVADGIKKSEDLINIILDNKAQTYHAKNQNDKQSGESDGKSGLGSAFYKHLM 300
            GK ++ RPVADG++K E LI+  L ++   Y A       + E    + +    YKHLM
Sbjct: 240 AGKRVLFRPVADGVRKPEVLIDEALSDRCPIYEA--DQSVATEEKAQPTSVWQTIYKHLM 297

Query: 301 GGVSQMLPFVIGGGIMIAIAFLFDNILGVPKDQLSNLGSYHEIAALFKNIGGAAFAFMLP 360
            GVS MLPF+IGGGIMIA+AFL D  +GVPKD L+ LGSYH  AA+FK IG AAF FMLP
Sbjct: 298 NGVSTMLPFIIGGGIMIALAFLIDQTMGVPKDHLAQLGSYHPAAAMFKQIGDAAFGFMLP 357

Query: 361 VLAGYIAYSIAEKPGLVAGFVAGSIASSGLAFGKVPFAEGGKATLALAGVPSGFLGALVG 420
           VLAG+IA SIA++PGLVAGFVAG++A++G A                     GFLGALVG
Sbjct: 358 VLAGFIASSIADRPGLVAGFVAGALANAGGA---------------------GFLGALVG 396

Query: 421 GFLAGGVILLLRKLLSGLPKSLEGIKSILLYPLLGVLITGFLMLLVNIPMAAINTALNTF 480
           GF AG ++L ++K+ S LP +L GI+S+LLYPL GV++TGF MLL+NIPM AIN ALN F
Sbjct: 397 GFAAGYLVLGVKKVFSYLPNALAGIRSVLLYPLFGVMVTGFAMLLINIPMKAINDALNGF 456

Query: 481 LQGLSGSSAVLMGLLVGGMMAVDMGGPVNKAAYVFGTGTLAATVANGGSVVMAAVMAGGM 540
           L G+SG+SAVL+G L+ GMMAVD+GGPVNKAAYVF TGTLAA+VA+GGSV+MAA MAGGM
Sbjct: 457 LNGMSGTSAVLLGALLAGMMAVDLGGPVNKAAYVFATGTLAASVASGGSVMMAATMAGGM 516

Query: 541 VPPLAVFVATLLFKDKFNNEERQSGLTNIVMGLSFITEGAIPFGAADPARAIPSFIVGSA 600
           VPPLA+FVAT LF++KF  EER +GL+NIVMGLSF+TEGAIPF AADP RAIPSFI+GSA
Sbjct: 517 VPPLAIFVATTLFRNKFTKEERDAGLSNIVMGLSFVTEGAIPFAAADPLRAIPSFIIGSA 576

Query: 601 LTGALVGLAGIKLMAPHGGIFVIALTSNPLLYILFILIGAVVSGVLFGLFRK 652
           +TG LVGL  IKLMAPHGGIFVI L S+P LY+  I +GAV+SGV+ GL +K
Sbjct: 577 VTGGLVGLMNIKLMAPHGGIFVIMLVSHPFLYLGLIALGAVISGVILGLLKK 628


Lambda     K      H
   0.319    0.137    0.379 

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: 1198
Number of extensions: 52
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 654
Length of database: 632
Length adjustment: 38
Effective length of query: 616
Effective length of database: 594
Effective search space:   365904
Effective search space used:   365904
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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