GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Rhodobacter johrii JA192

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  324 bits (830), Expect = 5e-93
 Identities = 195/489 (39%), Positives = 278/489 (56%), Gaps = 4/489 (0%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L    V++ +  V  L D    LR G VHAL G NGAGKST + IL G     AG +LL
Sbjct: 5   VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           +G PV F    EA AAG+ MI QE      +TV ENI+LGRE +R G  +D++A+   +R
Sbjct: 65  DGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKR-GPFLDHRAMQAESR 123

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
            LL+ L   VD  + +  LSV   Q+VEIAKA     +V+IMDEPT+ +   E  TL + 
Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245
           + RL A G  I+Y SH+L E+A+IAD  ++ RDG  V +     +  D +   +VG+EL+
Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243

Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305
            +        A    L+V  L+  G   D S  LR+GE+LG  GL+GSGR+E +  I GL
Sbjct: 244 GL-FPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGL 302

Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365
             A +G V ++G P+P     A   AG+  +TEDRK+ GL+L   +  N+ L A  R   
Sbjct: 303 RPA-TGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGR 361

Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425
             +  A +E  L +  +    I+     +   S+SGGNQQK++LAK +  EP  ++ DEP
Sbjct: 362 VLIDKAAEERALTQ-AISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEP 420

Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485
           TRGID G KQ+IY  + +    G + IVVSSE PE++ L++R+ V   GR+       A+
Sbjct: 421 TRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEAI 480

Query: 486 SQEALLRLA 494
           ++E ++RLA
Sbjct: 481 TEENIVRLA 489



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 56/224 (25%), Positives = 101/224 (45%), Gaps = 5/224 (2%)

Query: 22  LRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAA 81
           +RD   +LR G V    G  G+G++  +  ++G+     G + + G+P+     S A AA
Sbjct: 269 VRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLRPA-TGEVRMEGSPLPHASVSAARAA 327

Query: 82  GIAMITQELEPIPYMT---VAENIWLGREPRRAGCIVDNKALNRRTRELLDSLEFDV-DA 137
           G+  +T++ +    +    + EN+ L    R    ++D  A  R   + +   +  V D 
Sbjct: 328 GLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRVLIDKAAEERALTQAISDFDIRVGDR 387

Query: 138 TSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIV 197
                 LS    Q + +AK    + +V+I+DEPT  I     Q ++  I RL A+G  ++
Sbjct: 388 GISAGSLSGGNQQKLLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVI 447

Query: 198 YVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241
            VS  L E+  +A+   +   G          I  +++VR  +G
Sbjct: 448 VVSSELPEVIGLANRVVVMSAGRIAGEVEGEAITEENIVRLAMG 491


Lambda     K      H
   0.319    0.135    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: 595
Number of extensions: 41
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 495
Length of database: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
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 (21.8 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