GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Dinoroseobacter shibae DFL-12

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 3609577 Dshi_2961 ABC transporter related (RefSeq)

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Dino:3609577
          Length = 511

 Score =  336 bits (861), Expect = 1e-96
 Identities = 193/498 (38%), Positives = 303/498 (60%), Gaps = 8/498 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           ++++  +TK +   VAND V+ E+ +GE+HALLGENGAGKSTL+ ++ GL+ P  G +  
Sbjct: 4   LLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTF 63

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
            G       P  A + G+ MV QHF L +A TV ENI LG E        ++    +I +
Sbjct: 64  GGVPFAPPEPRAARSAGVAMVFQHFSLFEALTVAENIALGMEDPP----KMRDLAARITQ 119

Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185
           +S+ YGL ++P  L+  +S G++QRVEI++ L +   +LI DEPT+VLTP E+  L   +
Sbjct: 120 VSQAYGLPLDPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILFATL 179

Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245
           + L  EG +I+ I+HKL+EIRA+ D  T++R GK + T +  +K+ +ELAE+MVG+++  
Sbjct: 180 RKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKTLQQ 239

Query: 246 ITEKAAAQPKDVVLEIKDLNIKESRG-SLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
            T+ A       VLE++ L+   +      ++ +SL+VRAGE++G+ G+ GNGQ EL+ A
Sbjct: 240 -TKSAGNAFGAPVLELRGLSQPATTPFGTPLRDISLEVRAGEVLGIGGVAGNGQDELLSA 298

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           I+G  + +  +I LH   I+   P    +  V   PE+R       +M++ EN  L    
Sbjct: 299 ISGERRAED-AIFLHGTPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTENALLTGSV 357

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
           +  +++ GFLD+ K  + A  ++E FDVR  G   +A +LSGGN QK +I RE+ + P++
Sbjct: 358 REKLTRNGFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIGREVLQRPEV 417

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484
           LIV+QPT G+D  A   I + L+     G AV+VIS +LDE++ +SD  A ++ G++ G 
Sbjct: 418 LIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAALNGGRLSGK 477

Query: 485 VSPETTTKQELGILMVGG 502
           V     T +++G LM+GG
Sbjct: 478 VPAAGLTVEQIG-LMLGG 494



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 67/231 (29%), Positives = 107/231 (46%), Gaps = 16/231 (6%)

Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337
           +S ++  GE+  + G +G G++ LVK I GL + DSG++           PR      V 
Sbjct: 23  VSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTFGGVPFAPPEPRAARSAGVA 82

Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGE 397
            V +      L   +TVAENIAL           G  D  K+   A  + +     G   
Sbjct: 83  MVFQ---HFSLFEALTVAENIAL-----------GMEDPPKMRDLAARITQVSQAYGLPL 128

Query: 398 WVS--ASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKA 455
             S    +LS G +Q+  I R + + P LLI+ +PT  L    ++ +   L + RDEG A
Sbjct: 129 DPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILFATLRKLRDEGTA 188

Query: 456 VLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506
           +L IS +L+EI  + D   ++  G++     P   + +EL  +MVG  + +
Sbjct: 189 ILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKTLQQ 239


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: 580
Number of extensions: 25
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: 2
Length of query: 506
Length of database: 511
Length adjustment: 34
Effective length of query: 472
Effective length of database: 477
Effective search space:   225144
Effective search space used:   225144
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