GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Paraburkholderia bryophila 376MFSha3.1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate H281DRAFT_05270 H281DRAFT_05270 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Burk376:H281DRAFT_05270
          Length = 539

 Score =  463 bits (1192), Expect = e-135
 Identities = 234/500 (46%), Positives = 346/500 (69%), Gaps = 15/500 (3%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           PI+   G++  FPGVKAL  VD  L+PGEVH LMG+NGAGKST+I  LTGV   + G+I 
Sbjct: 34  PILATTGVSKTFPGVKALQRVDFRLFPGEVHTLMGQNGAGKSTLINVLTGVIAPDTGTIR 93

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           + G+   F    +A+ AG+ T+YQEVNLC NLSV EN+  G + R    IDW      A+
Sbjct: 94  LAGEVVAFASPQEAEAAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPDIKRRAQ 153

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
             LA++ + S+D    L +  IA+QQ+VAIARA+ ++A+VLILDEPTSSLD +EV  LF 
Sbjct: 154 AALARLDI-SLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDSEVAQLFK 212

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           I+R ++ SG+AILFV+HF++Q Y I+DR+T++RNG+   E + ++   D+L+  M+G   
Sbjct: 213 ILRHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARNLSADQLVAKMVGHE- 271

Query: 246 AELSQIGAKKARREITPG--------EKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGL 297
             +S+   + A     PG            ++++G+GK+GT+ P+D+++ +G+++G AGL
Sbjct: 272 -RMSERLREAAHEASAPGGTERGERAASAFIELRGVGKRGTLQPIDLNVERGQILGLAGL 330

Query: 298 LGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLT 357
           LGSGRTE  RLL+GAD+ DSGT  ++GK V +  P+ A+++ IAY  E+R+ EGI+ DL+
Sbjct: 331 LGSGRTETARLLFGADRADSGTMLVDGKPVRLRSPHDAVRHGIAYCAEDRKKEGIVADLS 390

Query: 358 VRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIG 417
           +R+NIL+ALQA RG ++ I ++ A  + D +++ L ++ +D ++P+  LSGGNQQK L+ 
Sbjct: 391 IRENILLALQARRGWWRKISRQRARELADLWIERLGIKASDAEQPIGLLSGGNQQKALLA 450

Query: 418 RWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV 477
           RWLAT P+LLILDEPTRGID+ AK +I   +L L + G+ ++FISSE+ EV+R+S  + V
Sbjct: 451 RWLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCANGLSILFISSEISEVLRVSHRVAV 510

Query: 478 LKDRHKIAEIE----NDDTV 493
           L+DR KIAE+E    N+D +
Sbjct: 511 LRDRRKIAEVEGKASNEDNI 530



 Score =  104 bits (259), Expect = 9e-27
 Identities = 66/236 (27%), Positives = 126/236 (53%), Gaps = 8/236 (3%)

Query: 15  IEFPGVK---ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ 71
           IE  GV     L  +DL +  G++  L G  G+G++   + L G  + ++G+++VDGKP 
Sbjct: 301 IELRGVGKRGTLQPIDLNVERGQILGLAGLLGSGRTETARLLFGADRADSGTMLVDGKPV 360

Query: 72  QFNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLGHEKRGPFG--IDWKKTHEAAKK 126
           +     DA   GIA   ++     +  +LS+ EN++L  + R  +   I  ++  E A  
Sbjct: 361 RLRSPHDAVRHGIAYCAEDRKKEGIVADLSIRENILLALQARRGWWRKISRQRARELADL 420

Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186
           ++ ++G+++ D   P+  +S   QQ   +AR +  + K+LILDEPT  +D     D+   
Sbjct: 421 WIERLGIKASDAEQPIGLLSGGNQQKALLARWLATDPKLLILDEPTRGIDVAAKFDIMDR 480

Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242
           +  +  +G++ILF+S  + ++  ++ R+ +LR+ + I EV  K +  D +  ++ G
Sbjct: 481 LLALCANGLSILFISSEISEVLRVSHRVAVLRDRRKIAEVEGKASNEDNIYRLIAG 536


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: 708
Number of extensions: 28
Number of successful extensions: 7
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: 513
Length of database: 539
Length adjustment: 35
Effective length of query: 478
Effective length of database: 504
Effective search space:   240912
Effective search space used:   240912
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