GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Azospirillum brasilense Sp245

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__azobra:AZOBR_RS06625
          Length = 511

 Score =  450 bits (1158), Expect = e-131
 Identities = 234/506 (46%), Positives = 333/506 (65%), Gaps = 6/506 (1%)

Query: 1   MAQH--VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPT 58
           M QH   +E R + K F    AN  ++L + KG IH ++GENGAGKST+M+++ G L   
Sbjct: 1   MPQHPPALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPAD 60

Query: 59  SGSIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKA 118
            G+I ++G  V + SP  +   GIGMVHQHFMLV+ FTV EN++LG E        + +A
Sbjct: 61  GGTILVDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAEGGVTLAAGMARA 120

Query: 119 GQEIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQ 178
             E+  L+  YGL VD +  + ++ VGAQQRVEILK LYRGADILI DEPT VLTP E  
Sbjct: 121 RTELTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETD 180

Query: 179 ELMTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMV 238
            L  I+++L ++GK++++ITHKL EI  + D VTV+RRG+ +  V  + T+ ++LAE+MV
Sbjct: 181 HLFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMV 240

Query: 239 GRSVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQS 298
           GR V   +EK P  P   +L +  L V +  G+  +KG+ L V+AGEI+GIAG+ GNGQS
Sbjct: 241 GRKVLLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQS 300

Query: 299 ELVQAITGLRKIKSGHLTIKGQDVT----KLSTRKITELSVGHVPEDRHRDGLILELTMA 354
           EL++A+ G+R    G + ++G+++T    + + R +  L VGHVPEDR R GL+      
Sbjct: 301 ELLEALAGMRPPAEGSVRLRGEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFEAQ 360

Query: 355 ENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIA 414
           E   L        +   +++   + +     M  +DVR  +  +PA  FSGGNQQK ++A
Sbjct: 361 ECAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVLA 420

Query: 415 REVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAV 474
           RE++R+PDLL+V QPTRG+D+GAIE+IH+RL+A RD+GKA+LLVS ELDEI  LSDRI V
Sbjct: 421 REMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILV 480

Query: 475 IHDGQIQGIVTPETTNKQELGILMAG 500
           + DG++ G V P   +++ LG++MAG
Sbjct: 481 MFDGRLVGEVAPGEADERRLGLMMAG 506



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 61/232 (26%), Positives = 112/232 (48%), Gaps = 10/232 (4%)

Query: 273 AIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITE 332
           A + +SL V  G I G+ G +G G+S ++  + G      G + + G+ V   S R    
Sbjct: 22  ANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTILVDGRPVAVRSPRDALA 81

Query: 333 LSVGHVPEDRHRDGLILE-LTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDV 391
             +G V    H+  ++++  T+ EN+ L       L+       +++    R    E D+
Sbjct: 82  AGIGMV----HQHFMLVDPFTVLENVLLGAEGGVTLAAGMARARTELTRLARDYGLEVDL 137

Query: 392 RGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDE 451
                 +P      G QQ+  I + + R  D+LI+ +PT  L     +++ + L A R++
Sbjct: 138 DRPVGELPV-----GAQQRVEILKALYRGADILILDEPTGVLTPQETDHLFRILRALREQ 192

Query: 452 GKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSI 503
           GK V++++ +L EI+ L+D + V+  GQ+   V    T+++EL  LM G  +
Sbjct: 193 GKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGRKV 244


Lambda     K      H
   0.315    0.135    0.363 

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: 32
Number of successful extensions: 6
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: 510
Length of database: 511
Length adjustment: 35
Effective length of query: 475
Effective length of database: 476
Effective search space:   226100
Effective search space used:   226100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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:

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