GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Dokdonella koreensis DS-123

Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate WP_067649690.1 I596_RS14985 ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_001632775.1:WP_067649690.1
          Length = 298

 Score =  101 bits (252), Expect = 3e-26
 Identities = 81/258 (31%), Positives = 130/258 (50%), Gaps = 15/258 (5%)

Query: 2   ANETVIQMID-VTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSE 60
           + ET+   +D V+KR+G  VA D V ++++ GE+ ALLG NGAGK+T + +L GL +P  
Sbjct: 3   STETIPARLDRVSKRYGGAVALDGVAVDIRAGELLALLGPNGAGKTTAIGLLLGLHQPDA 62

Query: 61  GEVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAK 120
           G V + G+       + AA   +G++ Q   + D   V E +    E+T+    +     
Sbjct: 63  GGVELFGQAPQ----TLAARREVGVMLQSAGIPDTLKVRELL----ELTRSYYAE----P 110

Query: 121 KKILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITE 180
           + I +     GL    + L   +S GQQ+RV+    L     +L  DEPT  L       
Sbjct: 111 RSIADCVALAGLDGLLERLYGRLSGGQQRRVQFALALCGRPRLLFLDEPTTGLDIEARMG 170

Query: 181 LMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVG 240
           L + ++ L+ +G +++L TH L+E  A+ADR+ V+ RG+ +    +     Q    L+  
Sbjct: 171 LWKAIRELVGQGCAVLLTTHYLEEAEALADRVVVLNRGRIVAEGSVAQIRAQVDRRLI-- 228

Query: 241 RSVSFITEKAAAQPKDVV 258
           R VS +T  A A    VV
Sbjct: 229 RCVSRLTAAAVAAWPGVV 246



 Score = 73.2 bits (178), Expect = 1e-17
 Identities = 59/218 (27%), Positives = 110/218 (50%), Gaps = 26/218 (11%)

Query: 267 KESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNK---DI 323
           K   G++ + G+++D+RAGE++ + G +G G+T  +  + GL + D+G ++L  +    +
Sbjct: 16  KRYGGAVALDGVAVDIRAGELLALLGPNGAGKTTAIGLLLGLHQPDAGGVELFGQAPQTL 75

Query: 324 TNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHA 383
             +R   +  QS G     + R+  +LE+T       ++YY  P S    +    ++   
Sbjct: 76  AARREVGVMLQSAGIPDTLKVRE--LLELT-------RSYYAEPRSIADCVALAGLDG-- 124

Query: 384 RELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIH 443
             L+E    R          LSGG Q++   A  +   P LL + +PT GLD+ A   + 
Sbjct: 125 --LLERLYGR----------LSGGQQRRVQFALALCGRPRLLFLDEPTTGLDIEARMGLW 172

Query: 444 KRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481
           K + +   +G AVL+ +  L+E   ++DR+ V++ G+I
Sbjct: 173 KAIRELVGQGCAVLLTTHYLEEAEALADRVVVLNRGRI 210


Lambda     K      H
   0.315    0.135    0.365 

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: 332
Number of extensions: 25
Number of successful extensions: 4
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: 506
Length of database: 298
Length adjustment: 30
Effective length of query: 476
Effective length of database: 268
Effective search space:   127568
Effective search space used:   127568
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: 50 (23.9 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