Alignments for a candidate for fruII-ABC in Kocuria flava HO-9041

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Kocuria flava HO-9041

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_058858172.1 AS188_RS06520 PTS transporter subunit EIIA

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_001482365.1:WP_058858172.1
          Length = 694

 Score =  703 bits (1814), Expect = 0.0
 Identities = 385/696 (55%), Positives = 477/696 (68%), Gaps = 19/696 (2%)

Query: 13  QIISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQSATGLPGGI 72
           ++I+ DL+ LD DLG  K  VI  L+  +  AGRA + D L   A+ARE ++ATG+PGGI
Sbjct: 3   ELITPDLVQLDQDLGEDKATVIGQLAALVQRAGRAEQLDGLLADAIAREDKTATGIPGGI 62

Query: 73  AIPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAEHMKLLSSLARAL 132
           AIPHCRS AV A +L  ARL PKVDFGA DGPADLVF IAAPEGA   H+KLL+ LAR+L
Sbjct: 63  AIPHCRSTAVTAPTLAMARLDPKVDFGAKDGPADLVFFIAAPEGADQTHLKLLAKLARSL 122

Query: 133 VRPAFVGALRDAKTPAEIVTLVNDVLAPAPA------ATPAAAAPAAAAAAAPAAAAAVP 186
           ++  F  +LR A++  E+V LV+  L   PA      AT AAA PAA AA   AA AA  
Sbjct: 123 MKKDFTASLRAARSEQEVVRLVDGALGLGPAEEGPAGATSAAATPAAVAAGGDAAGAA-- 180

Query: 187 APKPEPVAPEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQGS 246
                  APE+ P      + +VAVTACPTGIAHTYMAAD L  A +  GV + VETQGS
Sbjct: 181 -------APEQAPAAAGQRRRVVAVTACPTGIAHTYMAADGLSNAAQELGVDLQVETQGS 233

Query: 247 SGSTPLAPGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAGM 306
           +G T L P  IA A AVIFATDV V+ + RFAGKP VAS VKR I+EPD MI EAL    
Sbjct: 234 AGFTKLDPAAIAAADAVIFATDVDVRDRGRFAGKPYVASPVKRGIDEPDVMIREALARAE 293

Query: 307 NPSAAIVDAGSAGSAADEPAGSIGWGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGY 366
           +P A  V  G AG+     +G  GWGT +R+ ++TGVSYMIPFVAAGGLL+A GF++ G 
Sbjct: 294 DPDAPRVQGGGAGAEDAAASGQEGWGTRIRKAVMTGVSYMIPFVAAGGLLMAFGFMVAGA 353

Query: 367 EISGPAEDIVLSNSLGQLPEGGLATYLGAVLFQLGSLAFSFLVPALAGYIAFAIADRPGL 426
           +I+  A+D++ +++L  L E  L  YLGAVLF+ G+LA S LV ALAGYIA+ +ADRPG+
Sbjct: 354 DIANIADDVLGTSTLWNLGEFTLPQYLGAVLFKTGNLAMSLLVAALAGYIAYGLADRPGI 413

Query: 427 APGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVIIPLFATLIV 486
           APGF AG VA F+GAGF+GG+VGGL+AG+ A W+++  +P+W+  LMPVVIIPL A++  
Sbjct: 414 APGFAAGLVANFMGAGFLGGIVGGLLAGLAAYWLAKPQLPRWVGSLMPVVIIPLLASIFA 473

Query: 487 GALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLGIILGLMMCFDLGGPVNKAAYAFAVA 546
           G L+ LVLG P+A+  + LT  L+G++G+  + LG ILG MM FDLGGP+NK AY FA A
Sbjct: 474 GGLLLLVLGGPIATFMAWLTEQLSGMTGAGALALGAILGFMMGFDLGGPINKVAYTFAAA 533

Query: 547 GLNVNDPASL---RIMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAWLLGSAF 603
           GL     A+     IMAAV+AAGMVPPL +ALAS V +   FS  E+ENGKAAWLLG +F
Sbjct: 534 GLGAATAANTAPQEIMAAVIAAGMVPPLGLALASLVAK-RYFSTVEQENGKAAWLLGLSF 592

Query: 604 ISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFAIGNLLWFLVA 663
           ISEGAIPFAAADPLRV+P+ MAGGA  GA+ M   VT  APHGG+++   IGN L FL A
Sbjct: 593 ISEGAIPFAAADPLRVLPATMAGGAAAGAVAMGAAVTSPAPHGGVWILPIIGNPLMFLAA 652

Query: 664 LAAGVVVAALCVVGAKEFIKPGASDAELDPDVATVA 699
           +  G VV A  VV  K         A+ + DVA  A
Sbjct: 653 VLVGTVVTAGVVVALKHVGGVQRKVADTERDVAAAA 688


Lambda     K      H
   0.320    0.136    0.395 

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: 1350
Number of extensions: 68
Number of successful extensions: 4
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: 700
Length of database: 694
Length adjustment: 39
Effective length of query: 661
Effective length of database: 655
Effective search space:   432955
Effective search space used:   432955
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 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