GapMind for catabolism of small carbon sources

 

Aligments 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 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= TCDB::A2RKA7
         (506 letters)



>lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related
           (RefSeq)
          Length = 510

 Score =  290 bits (741), Expect = 1e-82
 Identities = 165/501 (32%), Positives = 281/501 (56%), Gaps = 13/501 (2%)

Query: 3   NETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGE 62
           ++  + +  +TK F    A   V+L L  G++ AL+GENGAGKST++ IL+G+ +P  G 
Sbjct: 17  SQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGR 76

Query: 63  VHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKK 121
           + V G+     +P  AA+ G+  +HQ  +L D  +V ENI LG+       L D K   +
Sbjct: 77  ILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTE 136

Query: 122 KILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITEL 181
               L    G  ++PD  ++D+ +  +  V I + L   A ++I DEPTA L+  EI EL
Sbjct: 137 NARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEEL 196

Query: 182 MQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR 241
            +++++L  +GK+I+ I+HK DEI  +AD  TV R G+ I    + D T  +L ++MVGR
Sbjct: 197 YELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGR 256

Query: 242 SVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTEL 301
            VS I  + A    D VL ++           +   +S  +R GEI+G  G+ G G++E 
Sbjct: 257 DVSQIFPQRAPNVGDTVLTVQGY-----AHPTEFDDISFTLREGEILGFYGLVGAGRSEF 311

Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361
           ++++ G+T+  +GS+++         P    +  + +VPEDR + G +L++ + +N+ L 
Sbjct: 312 MQSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLP 371

Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421
           +  +  +S+ GFL   +  + ARE  E  D+R A       +LSGGNQQK +IA+ +   
Sbjct: 372 SLGR--ISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATR 429

Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481
           P ++I+ +PT+G+D+G+   +H  + +   +G AV+++S E+ E+L +SDR+ V+ +G+I
Sbjct: 430 PRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRI 489

Query: 482 QGIVS-----PETTTKQELGI 497
              ++     PET  +   GI
Sbjct: 490 VAELAGDDLQPETLVRHAAGI 510



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 62/237 (26%), Positives = 118/237 (49%), Gaps = 9/237 (3%)

Query: 271 GSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRK 330
           G   +  +SL +  G++  + G +G G++ +VK +TG+ + D G I +  + +    P+ 
Sbjct: 32  GVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFSTPQA 91

Query: 331 ITEQSVGHVPEDRHRDGLVL-EMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEE 389
             +  V  +    H++ ++  E++VAENI L      P   +G +D+ K   +AR L+  
Sbjct: 92  AADHGVTAI----HQETVLFDELSVAENIFLG---HAPRGAFGLIDWKKTTENARALLTS 144

Query: 390 FDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQA 449
                  +      L   N+    IAR +     ++I+ +PT  L    IE +++ +   
Sbjct: 145 IGAELDPDH-KLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESL 203

Query: 450 RDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506
           + +GKA+L IS + DEI  ++D   V  DGQ+ G  +    T+ +L  +MVG ++++
Sbjct: 204 KAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260


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: 642
Number of extensions: 30
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: 510
Length adjustment: 34
Effective length of query: 472
Effective length of database: 476
Effective search space:   224672
Effective search space used:   224672
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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