GapMind for catabolism of small carbon sources

 

Alignments 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:

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:

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:

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:

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