GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Pantoea rwandensis LMG 26275

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_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_002095475.1:WP_084931811.1
          Length = 504

 Score =  318 bits (816), Expect = 2e-91
 Identities = 179/493 (36%), Positives = 288/493 (58%), Gaps = 10/493 (2%)

Query: 4   ETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEV 63
           + +I++ D+ K FG   A     L+++ GE+HALLGENGAGKSTLM +L G   P  G V
Sbjct: 3   QPLIELRDIVKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTV 62

Query: 64  HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123
           + KG+   I  P  A   GI ++HQ   L    TV ENI L +  T    +     + K 
Sbjct: 63  YDKGEAVQIKGPKAAMARGITLIHQEMALAQELTVAENIFLHDLPTF---IAWPKLRAKA 119

Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183
             +  R G  ++P A + D+SV  QQ VEI + L + A +++FDEPTAVL+  +   L++
Sbjct: 120 ANILRRLGFEIDPAATVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLE 179

Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV 243
           I+ +L   G +I+ I+H+LDE+  +ADR+T+++ G+ I T      T QE+  LMVGR V
Sbjct: 180 IISDLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIATESPQQTTLQEVIRLMVGRPV 239

Query: 244 -SFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELV 302
               +++A     + VL ++ LN +      KV+ +S  VRAGE+VG+ G+ G+G+TE+ 
Sbjct: 240 DQLFSDRATYGMGEEVLRVEKLNARR-----KVRDVSFSVRAGEVVGLGGLVGSGRTEVA 294

Query: 303 KAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQT 362
           + I G  + DSG I LH K ++ + P++  +  +  VPEDR R G+VL+M +  N+ +  
Sbjct: 295 RLIFGADRCDSGDIYLHGKKVSLRSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMAN 354

Query: 363 YYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNP 422
             K  M+  GF+  ++      +L ++  ++ AG     SSLSGGNQQK ++A+  +   
Sbjct: 355 -DKAVMAPLGFIHSSRETQVVSKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGG 413

Query: 423 DLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQ 482
            ++I+ +PTRG+DVGA   I++ + +   +G AV+VIS E  E+  + +R+ V+ +G I 
Sbjct: 414 QVIILDEPTRGVDVGAKREIYQLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAIC 473

Query: 483 GIVSPETTTKQEL 495
           G + P+  +++ L
Sbjct: 474 GELQPDDYSEENL 486



 Score = 95.1 bits (235), Expect = 5e-24
 Identities = 67/251 (26%), Positives = 128/251 (50%), Gaps = 16/251 (6%)

Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317
           ++E++D+ +K   G   +KG  L +RAGE+  + G +G G++ L++ + G    DSG++ 
Sbjct: 5   LIELRDI-VKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTVY 63

Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377
              + +  + P+    + +  + ++     L  E+TVAENI L            F+ + 
Sbjct: 64  DKGEAVQIKGPKAAMARGITLIHQEM---ALAQELTVAENIFLHDLPT-------FIAWP 113

Query: 378 KINSHARELMEE--FDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLD 435
           K+ + A  ++    F++  A    +   LS  +QQ   IAR + ++  +++  +PT  L 
Sbjct: 114 KLRAKAANILRRLGFEIDPAA---TVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLS 170

Query: 436 VGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQEL 495
                 + + +   R  G A++ IS  LDE+  ++DR+ ++ DGQ     SP+ TT QE+
Sbjct: 171 TQDANRLLEIISDLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIATESPQQTTLQEV 230

Query: 496 GILMVGGNINE 506
             LMVG  +++
Sbjct: 231 IRLMVGRPVDQ 241



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 47/220 (21%), Positives = 107/220 (48%), Gaps = 7/220 (3%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           V+  ++ GE+  L G  G+G++ +  ++ G      G++++ GK  ++ SP +A   GI 
Sbjct: 270 VSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCDSGDIYLHGKKVSLRSPQQAVKAGIA 329

Query: 85  MVHQHFM---LVDAFTVTENIILGNEVTKGINLDLKTAKKK---ILELSERYGLSVEP-D 137
           +V +      +V    +  N+ + N+      L    + ++   + +L+++  L      
Sbjct: 330 LVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVVSKLAQQMRLKCAGLH 389

Query: 138 ALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIIL 197
           A +  +S G QQ+V + K    G  ++I DEPT  +      E+ Q++  L ++G ++++
Sbjct: 390 APVSSLSGGNQQKVVLAKWFNLGGQVIILDEPTRGVDVGAKREIYQLIAELAQQGMAVVV 449

Query: 198 ITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAEL 237
           I+ +  E+  + +R+ V+  G     ++  D + + L  +
Sbjct: 450 ISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSM 489


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: 588
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 506
Length of database: 504
Length adjustment: 34
Effective length of query: 472
Effective length of database: 470
Effective search space:   221840
Effective search space used:   221840
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