GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Rhodobacter johrii JA192

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_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  300 bits (769), Expect = 6e-86
 Identities = 177/502 (35%), Positives = 285/502 (56%), Gaps = 13/502 (2%)

Query: 4   ETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEV 63
           E V+ +  V++ FG       V+ +L+ GE+HAL+GENGAGKST M IL+G L PS GEV
Sbjct: 3   EPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEV 62

Query: 64  HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123
            + G+  +  S  +A   G+ M+HQ F L    TV ENI LG E+ +G  LD +  + + 
Sbjct: 63  LLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAES 122

Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183
             L ER   +V+P A +  +SV  +Q VEI K L   A +LI DEPTAVLT  E   L++
Sbjct: 123 RRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLE 182

Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV 243
            +  L   G +I+  +HKLDE+  +ADR+TV+R G+ + T      +   +AE MVGR +
Sbjct: 183 QVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGREL 242

Query: 244 SFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVK 303
           S +    ++   + VLE+  L +        V+  S  +R GE++G AG+ G+G+TEL++
Sbjct: 243 SGLFPPKSSPAPEPVLEVAGLTVPGF-----VRDASFTLRRGEVLGFAGLVGSGRTELME 297

Query: 304 AITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTY 363
            I GL +  +G +++    + +          + ++ EDR   GL+L   + EN+ L   
Sbjct: 298 GIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLA- 355

Query: 364 YKPPMSKYG--FLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421
               + ++G   +D         + + +FD+R     +SA SLSGGNQQK ++A+ +   
Sbjct: 356 ----LDRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411

Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481
           P ++I+ +PTRG+DVG  + I+  + +   EG++V+V+S EL E++ +++R+ V+  G+I
Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471

Query: 482 QGIVSPETTTKQELGILMVGGN 503
            G V  E  T++ +  L +G N
Sbjct: 472 AGEVEGEAITEENIVRLAMGLN 493



 Score = 74.3 bits (181), Expect = 9e-18
 Identities = 55/228 (24%), Positives = 107/228 (46%), Gaps = 8/228 (3%)

Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337
           +  D+R GE+  + G +G G++  +K + G     +G + L  + +     R+     V 
Sbjct: 24  VDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLLDGRPVHFPSSREAEAAGVV 83

Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGE 397
            + ++ +   L   +TV ENI L    K    +  FLD+  + + +R L+E         
Sbjct: 84  MIHQEFN---LATPLTVEENIFLGRELK----RGPFLDHRAMQAESRRLLERLHC-AVDP 135

Query: 398 WVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVL 457
               S+LS  N+Q   IA+ +     +LI+ +PT  L     + + +++ + R  G A+L
Sbjct: 136 RARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQVDRLRAAGTAIL 195

Query: 458 VISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNIN 505
             S +LDE+  ++DR+ V+ DG+       +  ++  +   MVG  ++
Sbjct: 196 YTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243


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: 595
Number of extensions: 41
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: 499
Length adjustment: 34
Effective length of query: 472
Effective length of database: 465
Effective search space:   219480
Effective search space used:   219480
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