GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Pseudomonas fluorescens FW300-N2E3

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21385 AO353_21385 D-ribose
           transporter ATP-binding protein
          Length = 521

 Score =  337 bits (864), Expect = 6e-97
 Identities = 186/484 (38%), Positives = 296/484 (61%), Gaps = 17/484 (3%)

Query: 17  FPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGT 76
           FPGV AL  V L + PG V ALMGENGAGKST++K + G+Y+ +AG + + GKP  F+  
Sbjct: 37  FPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTP 96

Query: 77  LDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAKKYLAQMGLES 135
           L A  AGIA ++QE+NL  ++S+ EN+ +G E+   F  ID ++ H    + L ++ + +
Sbjct: 97  LAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLERLRI-N 155

Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195
           +DP   + ++SIA +Q+V IA+A+  ++ +LI+DEPTS++   EV  LF+I+  ++  G 
Sbjct: 156 LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGK 215

Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQIGAKK 255
            I++++H +++++ I D + + R+G +I          D LI MM+G+   ELSQ+   +
Sbjct: 216 GIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR---ELSQLFPVR 272

Query: 256 ARREITPGEKPIVD----VKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYG 311
                   EKPI D    V+ L   G    V  D++ GE++G AGL+GSGRT +   ++G
Sbjct: 273 --------EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFG 324

Query: 312 ADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRG 371
               D G   L+G+ V ISDP+ A++   A  TE+R+  G+   L+V +N+ +A+     
Sbjct: 325 ITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYA 384

Query: 372 MFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDE 431
               I +K   A+ +   K+L V+    ++ +  LSGGNQQK L+ RWL T+P +LILDE
Sbjct: 385 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDE 444

Query: 432 PTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDD 491
           PTRGID+GAKAEI +++  LAS+GM V+ ISSEL EV+ +SD + V+ +   +  ++  +
Sbjct: 445 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 504

Query: 492 TVSQ 495
              +
Sbjct: 505 ATQE 508



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 65/242 (26%), Positives = 123/242 (50%), Gaps = 10/242 (4%)

Query: 244 SAAELSQIGAKKARREITPGEKP----IVDV-KGLGKKGTINPVDVDIYKGEVVGFAGLL 298
           ++A  S I     +    P ++P    I++V KG      ++ V + +  G V+   G  
Sbjct: 3   ASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGEN 62

Query: 299 GSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTV 358
           G+G++ L +++ G  +PD+G   L GK V    P  AL+  IA      ++  ++  +++
Sbjct: 63  GAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMI---HQELNLMPHMSI 119

Query: 359 RQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418
            +NI I  +   G F  I  +E      + ++ L +   DP+  V NLS   +Q V I +
Sbjct: 120 AENIWIGREQLNG-FHMIDHREMHRCTAQLLERLRIN-LDPEEQVGNLSIAERQMVEIAK 177

Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
            ++   ++LI+DEPT  I     A +  ++ DL +QG G+++I+ ++ EV  ++D++ V 
Sbjct: 178 AVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVF 237

Query: 479 KD 480
           +D
Sbjct: 238 RD 239



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 52/226 (23%), Positives = 112/226 (49%), Gaps = 7/226 (3%)

Query: 25  GVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGI 84
           GV   L+ GE+  + G  G+G++ + +A+ G+   + G I +DG+P + +    A   G 
Sbjct: 294 GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGF 353

Query: 85  ATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDP 138
           A + ++  L      LSV EN+   +L H     F I  K      +    ++ +++   
Sbjct: 354 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGF-IQQKALRALCEDMCKKLRVKTPSL 412

Query: 139 HTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAIL 198
              + ++S   QQ   +AR ++ N ++LILDEPT  +D     +++ ++  +   G+A++
Sbjct: 413 EQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVI 472

Query: 199 FVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244
            +S  L ++  ++DR+ ++  G  +  +   +  ++ ++ +  G S
Sbjct: 473 MISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 518


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: 636
Number of extensions: 29
Number of successful extensions: 8
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: 521
Length adjustment: 35
Effective length of query: 478
Effective length of database: 486
Effective search space:   232308
Effective search space used:   232308
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 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