GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pantoea rwandensis LMG 26275

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_084931762.1 HA51_RS02835 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_002095475.1:WP_084931762.1
          Length = 500

 Score =  395 bits (1014), Expect = e-114
 Identities = 213/502 (42%), Positives = 331/502 (65%), Gaps = 10/502 (1%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L  +GI K +   +A+ +VDF V   E+ +LIGENGAGKSTL+ IL+GV   D+G I VN
Sbjct: 6   LMMRGITKTYGSAIALQDVDFMVRPGEVHALIGENGAGKSTLLNILSGVRPADSGAIHVN 65

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSR-VDENYM 133
           GE+V+  +P+ A   GI++IHQEL     ++VA+N+FL          TL+   VD+   
Sbjct: 66  GEQVQMKNPLSARHAGIAMIHQELQHVPELSVAQNMFLGRPLT-----TLNGLFVDKRAQ 120

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
             R+  +L  +    +P   ++NL  +Q+Q+VEI +AL+ E +II MDEPTSSLT  E E
Sbjct: 121 LARATHILKQLDPSINPAEPIKNLKVSQQQIVEIARALLDEAKIIAMDEPTSSLTPREFE 180

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
           RL E+I  LKS G+S+++VSH+++E+ ++ DR  +MRDG+++G +   +   +TI+  MV
Sbjct: 181 RLAELIADLKSTGVSLIYVSHKMNEIFQVCDRATIMRDGRQVGVVNICDETEETIVAKMV 240

Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313
           GR+++   H       ++ L+V N+    ++K  SF V  GEVLG AGLVGAGRTE + L
Sbjct: 241 GRKIDKQAHQSWATDRKV-LQVENVARGTEIKPASFSVCAGEVLGVAGLVGAGRTELLKL 299

Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373
           + G++++ +G++ VNG+ V   N   AI+ GIGL+PEDRK +G++    VK N+ LPS++
Sbjct: 300 IAGIDKRSAGEVRVNGQLVRNHNVSAAIRAGIGLVPEDRKKEGIIKARAVKVNMALPSMR 359

Query: 374 KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADIL 433
             +  G V+ + K   ++++ +  L ++  +I +    LSGGNQQKV++ +W+A +A++ 
Sbjct: 360 NFTLAG-VIRKVKLNAVAQEVMSDLKLRPLNIEKPIGTLSGGNQQKVIIGRWVAADAEVF 418

Query: 434 IFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVL 493
           +FDEPTRGID+GAKAEI+ +I +LA QGKA++++SSE+ EIL +SDR++VM EG+IT  L
Sbjct: 419 LFDEPTRGIDIGAKAEIYNLIEKLAQQGKAIVVVSSEMTEILRVSDRVLVMREGKITREL 478

Query: 494 DNREKRVTQEEIMYYASGQKKQ 515
              +  +T+E I  +A    K+
Sbjct: 479 TGDD--ITEENIARFAINDIKE 498


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: 643
Number of extensions: 36
Number of successful extensions: 9
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: 500
Length adjustment: 34
Effective length of query: 486
Effective length of database: 466
Effective search space:   226476
Effective search space used:   226476
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 24 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