GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Azospirillum brasilense Sp245

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  332 bits (850), Expect = 3e-95
 Identities = 193/497 (38%), Positives = 307/497 (61%), Gaps = 25/497 (5%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA--GS 63
           PI+ MKGIT  FPGVKALD V+L++  GE+HAL+GENGAGKST++K L+GVY   +  G 
Sbjct: 4   PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63

Query: 64  IMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA 123
           I   G+PQ F G  D++  GI  ++QE+ L   LS+ EN+ LG+E+     IDW      
Sbjct: 64  IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLR 123

Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183
           A++ L  +GL    P T ++ I +  QQLV IA+A+    K+LILDEPT+SL+ ++   L
Sbjct: 124 ARELLRLVGLHD-PPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDAL 182

Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDT--PRDELIGMMI 241
             ++ + +  G+A + +SH L++I ++ DR+TILR+G  ++ +  ++    +D +I  M+
Sbjct: 183 LELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMV 242

Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINP-------VDVDIYKGEVVGF 294
           G++ ++      +  RR   PG+  + +VKG       +P       V++ + +GEVVG 
Sbjct: 243 GRALSD------RYPRRTTVPGDV-LFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGI 295

Query: 295 AGLLGSGRTELGRLLYGAD--KPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGI 352
           AGL+G+GRTE    L+G    +   G   L+G+++++S    A+ N +AY+TE+R+  G+
Sbjct: 296 AGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGL 355

Query: 353 IGDLTVRQNILIALQATRGMFKP--IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGN 410
           + D  +R N+ +A    RG+ K   I  +    + +++ + L +R AD  +   NLSGGN
Sbjct: 356 VLDNDIRHNVTLA--NLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGN 413

Query: 411 QQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVR 470
           QQKV++ +WL   P++LILDEPTRGID+GAK EI  ++  L ++G GVV ISSE+ E++ 
Sbjct: 414 QQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLG 473

Query: 471 LSDDIEVLKDRHKIAEI 487
           ++D I V+     +AE+
Sbjct: 474 VADRIYVMNAGEMVAEM 490



 Score = 74.7 bits (182), Expect = 7e-18
 Identities = 54/233 (23%), Positives = 117/233 (50%), Gaps = 11/233 (4%)

Query: 18  PGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTG-VYKINA-GSIMVDGKPQQFNG 75
           PG + +  V+LT+  GEV  + G  GAG++    +L G  Y  N  G   +DG+    + 
Sbjct: 275 PGRRVVRDVNLTVRRGEVVGIAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVST 334

Query: 76  TLDAQNAGIATVYQE---VNLCTNLSVGENVML----GHEKRGPFGIDWKKTHEAAKKYL 128
              A   G+A   ++   + L  +  +  NV L    G  KR  + ID ++  + A+++ 
Sbjct: 335 ISRAMANGLAYATEDRKHLGLVLDNDIRHNVTLANLRGVAKR--WVIDHEREVQVAEEFR 392

Query: 129 AQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMR 188
            ++ +   D      ++S   QQ V +++ +  + +VLILDEPT  +D     +++ I+ 
Sbjct: 393 RRLRIRCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIIN 452

Query: 189 KVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
           ++   G  ++ +S  + ++  + DR+ ++  G+ + E+   +  +++++G ++
Sbjct: 453 QLVAEGRGVVLISSEMPELLGVADRIYVMNAGEMVAEMPAAEASQEKIMGAIM 505



 Score = 63.2 bits (152), Expect = 2e-14
 Identities = 56/254 (22%), Positives = 118/254 (46%), Gaps = 39/254 (15%)

Query: 266 PIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321
           PI+++KG+ K       ++ V++ + +GE+    G  G+G++ L ++L       SG Y 
Sbjct: 4   PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVL-------SGVY- 55

Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGI-----IGDLTVRQNILIA--LQATRGMFK 374
                     P  +   +I +  + +   GI     +G + + Q + +   L  T  +F 
Sbjct: 56  ----------PQGSFDGEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFL 105

Query: 375 PIPKKEADAIVDKYMKELNVRPA--------DPDRPVKNLSGGNQQKVLIGRWLATHPEL 426
              ++ +  ++D     L  R           P+  + ++  G QQ V I + L+   +L
Sbjct: 106 G-NEQASRGVIDWDAATLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKL 164

Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486
           LILDEPT  ++      + +++L   ++G+  + IS +L E+ +++D + +L+D   +  
Sbjct: 165 LILDEPTASLNESDSDALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVET 224

Query: 487 IE-NDDTVSQATIV 499
           ++  +  VSQ  I+
Sbjct: 225 LDCREAVVSQDRII 238


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: 692
Number of extensions: 44
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 513
Length of database: 518
Length adjustment: 35
Effective length of query: 478
Effective length of database: 483
Effective search space:   230874
Effective search space used:   230874
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