Aligments for a candidate for fruK in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments 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:

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