Alignments for a candidate for xylK_Tm in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Pseudomonas simiae WCS417

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__WCS417:GFF4164
          Length = 499

 Score =  352 bits (903), Expect = e-101
 Identities = 194/480 (40%), Positives = 293/480 (61%), Gaps = 7/480 (1%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L+  GI K FPGV A+  + FE    E+ +L+GENGAGKSTL+KIL G   P +G + + 
Sbjct: 6   LRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQIG 65

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
            + ++F S  D+   G++VIHQEL+L   MTVAEN+FL      G   T    V+ + + 
Sbjct: 66  EQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFL------GHLPTRFGVVNRSQLR 119

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
            ++   L  +  +  PD  +  L+  QRQ+VEI KAL +   +I  DEPTSSL+  E +R
Sbjct: 120 KQALACLKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDR 179

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKK-GEFDVDTIIKMMV 253
           L  II  L+  G  V++VSHR++EV RI + + V +DG+ +           D ++  MV
Sbjct: 180 LMAIITRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMNALSHDQLVTCMV 239

Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313
           GR+++      +   GE+AL+V  L      + VS  V KGE+LG  GLVGAGRTE   L
Sbjct: 240 GRDIQDIYDYRQREQGEVALKVEGLLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRL 299

Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373
           + G+ +  +G + + G+ +++++P DAI  G+ L PEDRK +G++   +V +NI + +  
Sbjct: 300 LSGLTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARG 359

Query: 374 KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADIL 433
             S +G +L +  E   ++  +K + +KTP+  Q    LSGGNQQK +L +WL+    +L
Sbjct: 360 AHSTFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVL 419

Query: 434 IFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVL 493
           + DEPTRGID+GAK+EI+++I  LAA G AVI++SS+L E++ +SDRI+VM EG +T  L
Sbjct: 420 LLDEPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGEL 479



 Score = 98.2 bits (243), Expect = 6e-25
 Identities = 69/246 (28%), Positives = 131/246 (53%), Gaps = 13/246 (5%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           LK +G++   PG+   + V   V++ EI+ L G  GAG++ L ++L+G+ +  AG + + 
Sbjct: 259 LKVEGLLG--PGLR--EPVSLNVHKGEILGLFGLVGAGRTELFRLLSGLTRSTAGSLALC 314

Query: 75  GERVEFHSPVDAFKKGISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDEN 131
           G+ ++  SP DA   G+ +  ++     +    +VAENI ++    RG   T    + + 
Sbjct: 315 GQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINIS---ARGAHSTFGWLLRDG 371

Query: 132 YMYTRSKELLDLIGAKFSPDA--LVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTV 189
           +  T +   +  +  K +P+A   +  L+   +Q   + + L    +++ +DEPT  + +
Sbjct: 372 WETTNADRQIKAMKVK-TPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDI 430

Query: 190 EETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249
                +++II  L + GI+V+ VS  L EVM ISDRI+VM +G   GEL + + D   ++
Sbjct: 431 GAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTRDQADEARLL 490

Query: 250 KMMVGR 255
           ++ + R
Sbjct: 491 QLALPR 496



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 55/212 (25%), Positives = 104/212 (49%), Gaps = 7/212 (3%)

Query: 284 VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKM 343
           +  +SFE R  EV    G  GAG++  + ++ G     SG + +  + ++ K+  D+I  
Sbjct: 21  LSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQIGEQTMDFKSAADSIAC 80

Query: 344 GIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTP 403
           G+ +I ++  L   V  MTV +N+ L  L   +R+G+V   +  ++     +K L+ +  
Sbjct: 81  GVAVIHQELHL---VPEMTVAENLFLGHLP--TRFGVVNRSQLRKQALA-CLKGLADEID 134

Query: 404 SIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKA 463
              ++   LS G +Q V +AK L+  A ++ FDEPT  +       +  +I  L  +GK 
Sbjct: 135 PDEKLGR-LSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIITRLRDEGKV 193

Query: 464 VIMISSELPEILNLSDRIVVMWEGEITAVLDN 495
           V+ +S  + E+  + + + V  +G      D+
Sbjct: 194 VLYVSHRMEEVFRICNAVTVFKDGRYVRTFDD 225


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: 619
Number of extensions: 32
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: 499
Length adjustment: 34
Effective length of query: 486
Effective length of database: 465
Effective search space:   225990
Effective search space used:   225990
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:

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
the source code
instructions for running GapMind on your computer

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