GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Dethiosulfovibrio salsuginis USBA 82

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 WP_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_900177735.1:WP_085545256.1
          Length = 503

 Score =  435 bits (1118), Expect = e-126
 Identities = 222/499 (44%), Positives = 336/499 (67%), Gaps = 2/499 (0%)

Query: 8   MREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGS 67
           M+ ITK F    AND I+L L+KGE+ ALLGENGAGKSTLMN+L+G+  P  G+I I G+
Sbjct: 1   MKGITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGT 60

Query: 68  AVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKALSE 127
            ++  SP+ +   GIGMVHQHFMLV + TV EN++LG   +   IL   K   EI A+S+
Sbjct: 61  RLSFRSPNDAISAGIGMVHQHFMLVPSQTVWENMVLGLPDLPQ-ILPKGKIISEITAISK 119

Query: 128 KYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSL 187
           +YGL VDP A I  +S+G QQRVEILKTLYR A +LI DEPTAVLTP E + L   +K +
Sbjct: 120 QYGLEVDPEAIIWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKRM 179

Query: 188 VKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSFTIE 247
            +EG+ II I+HKLDE+  ++DRVTV+R+GK I TV+    + + +AEMMVG+ ++  ++
Sbjct: 180 TEEGRGIIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEMMVGKRINLDLD 239

Query: 248 KTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGL 307
           K    P E + S+       +RG+ A+  +SLE++ G+I+G+AG+ GNGQ+EL Q + GL
Sbjct: 240 KKDITPGEVVYSLSQANAISDRGLKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGL 299

Query: 308 RKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPL 367
           RK+ SG L +KG++VT  S R++ +  + ++P DR   G++  + + EN  L+ Y++ P+
Sbjct: 300 RKMTSGKLILKGKEVTDSSPRELIDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPV 359

Query: 368 SHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVS 427
           +   ++++  + +H   +++ F+V   +   P +  SGGN QK ++ RE+   P +LI  
Sbjct: 360 ARGVLIDWKAVLKHALGIVKNFNVDTPSVETPVRNLSGGNIQKLMLGRELSDIPKVLIAM 419

Query: 428 QPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIV-TP 486
            PT GLDV A  ++ ++L+ ER++G A+ L+S +LDE+++LSDRIAV++ G+I G+V  P
Sbjct: 420 NPTWGLDVAATRFVREQLLEEREKGAAIFLISEDLDELMSLSDRIAVMYRGKIMGLVEDP 479

Query: 487 ETTNKQELGILMAGGSIER 505
            T   + +G++MAG  IE+
Sbjct: 480 NTFGIERIGMMMAGTRIEQ 498


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: 649
Number of extensions: 32
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: 510
Length of database: 503
Length adjustment: 34
Effective length of query: 476
Effective length of database: 469
Effective search space:   223244
Effective search space used:   223244
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 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