GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N2C3

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20250
          Length = 514

 Score =  354 bits (908), Expect = e-102
 Identities = 193/480 (40%), Positives = 296/480 (61%), Gaps = 7/480 (1%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L+  GI K FPGV A+ N+ F  +  ++ +L+GENGAGKSTL+KIL G   P +G++ + 
Sbjct: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
            + + F    D+   G++VIHQEL+L   MTVAEN+FL +   R         V+   + 
Sbjct: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR------FGLVNRGVLR 129

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
            ++  LL  +  +  P   V  L+  QRQ+VEI KAL +   +I  DEPTSSL+  E +R
Sbjct: 130 QQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDR 189

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKK-GEFDVDTIIKMMV 253
           L  II  L+  G  V++VSHR++EV RI + + V +DG+ +   +   E   D ++  MV
Sbjct: 190 LMAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMV 249

Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313
           GR+++          G++AL+V++L      + VSF+V KGE+LG  GLVGAGRTE   L
Sbjct: 250 GRDIQDIYDYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRL 309

Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373
           + G+ ++  G + ++G+++++++P DAI  G+ L PEDRK +G++   +V +NI + +  
Sbjct: 310 LSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369

Query: 374 KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADIL 433
             S  G +L    E   ++  +K L +KTP+  Q    LSGGNQQK +L +WL+    +L
Sbjct: 370 AHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVL 429

Query: 434 IFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVL 493
           + DEPTRGID+GAKAEI+++I  LAA G AVI++SS+L E++ +SDRI+V+ EG +   L
Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 61/239 (25%), Positives = 120/239 (50%), Gaps = 5/239 (2%)

Query: 21  VKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEF 80
           VK   G    + V F+V++ EI+ L G  GAG++ L ++L+G+ +   G ++++G+ ++ 
Sbjct: 271 VKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLVLHGKELKL 330

Query: 81  HSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRS 137
            SP DA   G+ +  ++     +    +V ENI ++          L     E       
Sbjct: 331 RSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSALGCLLRGDWERG--NAD 388

Query: 138 KELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFE 197
           K++  L     +    +  L+   +Q   + + L    +++ +DEPT  + +     +++
Sbjct: 389 KQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQ 448

Query: 198 IIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGRE 256
           II  L + GI+V+ VS  L EVM ISDRI+V+ +G   GEL + + +   ++++ + R+
Sbjct: 449 IIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 507



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 59/231 (25%), Positives = 113/231 (48%), Gaps = 8/231 (3%)

Query: 286 NVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGI 345
           N+SF    G+V    G  GAG++  + ++ G     SGD+ +  + +  K   D+I  G+
Sbjct: 33  NISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTMAFKGTADSIASGV 92

Query: 346 GLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSI 405
            +I ++  L   V  MTV +N+ L  L   +R+GLV +     + +   +K L+ +    
Sbjct: 93  AVIHQELHL---VPEMTVAENLFLGHLP--ARFGLV-NRGVLRQQALTLLKGLADEIDPQ 146

Query: 406 YQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVI 465
            ++   LS G +Q V +AK L+  A ++ FDEPT  +       +  +I  L  +GK V+
Sbjct: 147 EKVGR-LSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIARLRDEGKVVL 205

Query: 466 MISSELPEILNLSDRIVVMWEGEITAVLDNREKRVTQEEIMYYASGQKKQN 516
            +S  + E+  + + + V  +G      +N  + +T ++++    G+  Q+
Sbjct: 206 YVSHRMEEVFRICNAVTVFKDGRYVRTFENMSE-LTHDQLVTCMVGRDIQD 255


Lambda     K      H
   0.319    0.138    0.381 

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: 644
Number of extensions: 37
Number of successful extensions: 7
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: 520
Length of database: 514
Length adjustment: 35
Effective length of query: 485
Effective length of database: 479
Effective search space:   232315
Effective search space used:   232315
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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