Aligments for a candidate for fruK in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruK in Dyella japonica UNC79MFTsu3.2

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  427 bits (1098), Expect = e-124
 Identities = 228/501 (45%), Positives = 331/501 (66%), Gaps = 10/501 (1%)

Query: 6   PIVVM-KGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSI 64
           P+V+  +G+   F    ALDGVDL L  GEVHALMG+NGAGKST+IK LTGV + + GS+
Sbjct: 10  PVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSV 69

Query: 65  MVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGH--EKRGPFGIDWKKTHE 122
            +DG+    +  ++AQ  GI TVYQEVNLC NLSV EN+  G    +R    IDW++  +
Sbjct: 70  ELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRD 129

Query: 123 AAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182
            A+  L Q+ LE +D   PL S  +A++Q+VAIARA+ ++A+VLILDEPTSSLD  EVR+
Sbjct: 130 GARSLLRQLHLE-LDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRE 188

Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242
           LF ++ ++R+ G+AILFV+HFLDQ+Y ++DR+T+LR+G  + E    D P   L+  M+G
Sbjct: 189 LFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVG 248

Query: 243 KSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGR 302
           +   +L  +    A R   P   P +D +GLG +G ++PVD+ + +GE++G  GLLGSGR
Sbjct: 249 R---DLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGR 305

Query: 303 TELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI 362
           TEL RLL+G D+ + G   + G++V +  P  A+   +A   E R+ +GI+ +L+VR+NI
Sbjct: 306 TELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENI 365

Query: 363 LIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422
           ++ALQA +G ++ + +   D +  + ++ L ++ AD + PV  LSGGNQQKV++ RWL T
Sbjct: 366 VLALQARQG-WRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVT 424

Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRH 482
            P LLILDEPTRGID+ AK E+   V   A  GM V+FIS+E  E+ R  D I V+++R 
Sbjct: 425 EPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERR 484

Query: 483 KIAEIENDDTVSQATIVETIA 503
           K  E+    T  +A ++  IA
Sbjct: 485 KAGELPGGST--EARVLAMIA 503


Lambda     K      H
   0.316    0.135    0.376 

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: 660
Number of extensions: 36
Number of successful extensions: 8
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: 513
Length of database: 505
Length adjustment: 34
Effective length of query: 479
Effective length of database: 471
Effective search space:   225609
Effective search space used:   225609
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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, or view the source code.

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