GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylK_Tm in Pseudomonas fluorescens GW456-L13

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:Q9WXX0
         (520 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  354 bits (909), Expect = e-102
 Identities = 197/504 (39%), Positives = 307/504 (60%), Gaps = 9/504 (1%)

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

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
              ++F S  D+   G++VIHQEL+L   MTVAEN+FL      G        ++ + + 
Sbjct: 76  ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFL------GHLPASFGLINRSTLR 129

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

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

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

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

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

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

Query: 494 DNREKRVTQEEIMYYASGQKKQNG 517
               ++  +  ++  A  +++ +G
Sbjct: 490 S--REQANESNLLQLALPRQRADG 511


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: 652
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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