GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Rhodobacter johrii JA192

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  337 bits (864), Expect = 6e-97
 Identities = 200/499 (40%), Positives = 298/499 (59%), Gaps = 13/499 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L  + + + F  V  + +VDF++   E+ +LIGENGAGKST +KIL G L P AGE+L+
Sbjct: 5   VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
           +G  V F S  +A   G+ +IHQE NL   +TV ENIFL  E  RG        +D   M
Sbjct: 65  DGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPF------LDHRAM 118

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
              S+ LL+ +     P A V  L+   RQMVEI KAL  + R++ MDEPT+ LT  ET+
Sbjct: 119 QAESRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETD 178

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            L E ++ L++ G ++++ SH+LDEV RI+DR+ V+RDG+R+          D + + MV
Sbjct: 179 TLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMV 238

Query: 254 GREVE-FFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312
           GRE+   FP      P E  LEV  L     V++ SF +R+GEVLGFAGLVG+GRTE M 
Sbjct: 239 GRELSGLFPPKSSPAP-EPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELME 297

Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372
            + G+ +  +G++ + G  +   +   A   G+  + EDRK +GL+L   + +N+ L +L
Sbjct: 298 GIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLAL 356

Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432
            +  R  +++D+  EE      +    I+         +LSGGNQQK++LAK +     +
Sbjct: 357 DRFGR--VLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRV 414

Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492
           +I DEPTRGIDVG K +I+  I  LAA+G++VI++SSELPE++ L++R+VVM  G I   
Sbjct: 415 VIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGE 474

Query: 493 LDNREKRVTQEEIMYYASG 511
           ++   + +T+E I+  A G
Sbjct: 475 VEG--EAITEENIVRLAMG 491


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: 673
Number of extensions: 32
Number of successful extensions: 8
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: 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 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