GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Paucidesulfovibrio gracilis DSM 16080

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_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  342 bits (877), Expect = 2e-98
 Identities = 194/498 (38%), Positives = 305/498 (61%), Gaps = 13/498 (2%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           ++ ++ +TK+F   VAND I+L++  G + ALLGENGAGKSTLM+MLAG  +P +G+I +
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124
           +G  V   S   + + GIGMV+QHFMLVE+ TV EN++LG E   +  L+ K+    ++ 
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE--GSFFLNPKEMRNRVQE 141

Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184
           LS +YGL +DP A+++D+S+G +QRVEILK LYR + +LIFDEPTAVLTP E   L   +
Sbjct: 142 LSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEAL 201

Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGK-SIETVEVSGTTSQDLAEMMVGRSVS 243
             + ++GKSI+ I+HKL+E+ +VAD + ++R+G+   E  E   T+  DLA  MVG+ V 
Sbjct: 202 WKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEVL 261

Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303
             +++      + +L +++L      GI  ++ ++ ++  GE++ + G+ GNGQ  LV+A
Sbjct: 262 LEVDREAMPHGDAVLQVRNLT-----GI-GLEDITFDLHQGEVVAVVGVAGNGQKALVEA 315

Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYY 363
           I GLRK     + I G+       +   + S+ ++PEDR        L + +NL L T  
Sbjct: 316 ICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTT-- 373

Query: 364 KAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDL 423
           +   +    L+  K       L+++FD+R       A   SGGN QK+++ARE+ R P L
Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433

Query: 424 LIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGI 483
           ++  QPT+GLD+ A E +   L+A R E   +LLV+ +L+E L L+DR+AVI+ G+   +
Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLLAAR-EMAGILLVTGDLNEALQLADRVAVIYRGRFMDV 492

Query: 484 VTPETTNK-QELGILMAG 500
            +     K   +G++MAG
Sbjct: 493 FSVSDKQKVNRIGLMMAG 510


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: 554
Number of extensions: 28
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 510
Length of database: 514
Length adjustment: 35
Effective length of query: 475
Effective length of database: 479
Effective search space:   227525
Effective search space used:   227525
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 Apr 09 2024. 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