GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupA in Phaeobacter inhibens BS107

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 GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= TCDB::A2RKA7
         (506 letters)



>lcl|FitnessBrowser__Phaeo:GFF2274 PGA1_c23060 ribose import
           ATP-binding protein RbsA
          Length = 503

 Score =  285 bits (728), Expect = 3e-81
 Identities = 173/491 (35%), Positives = 269/491 (54%), Gaps = 8/491 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           V+++  + K F    A D V+L +  GE+HAL+GENGAGKSTLM +L G+ +P EG++ V
Sbjct: 7   VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKKKIL 124
             +   +  P  A   GI  +HQ   L D  +V ENI LG    K   L D    + K  
Sbjct: 67  AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126

Query: 125 ELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184
            + E+  +       + D+S+  QQ VEI + L   A  +IFDEPTA LT AE   L ++
Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244
           + +L ++G  I  I+H+++EI  + DRI+V+R G+   TV   +   + + ++M+GR + 
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246

Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
               +A  +  +V LE++ L    S GSL  + ++ +VR GE+VG  G+ G G+TE+ + 
Sbjct: 247 LSRNEAHHELGEVALEVRGL----SCGSL-FEDVNFEVRRGEVVGFYGLVGAGRTEIAET 301

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           + GL    SGSI L   ++    P    E+ +  VPEDR   GLVL M   +N+ L    
Sbjct: 302 LFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQV- 360

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
              +    F+      +   +  ++ D+R  G      +LSGGNQQK +I + +   P++
Sbjct: 361 -DDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNV 419

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484
           LIV +PTRG+DVG+   IH  L     +G AV+VIS E+ E+L+V+DRI  ++ G+I   
Sbjct: 420 LIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRT 479

Query: 485 VSPETTTKQEL 495
            + E  T++ L
Sbjct: 480 FTSEEVTEENL 490



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 61/240 (25%), Positives = 119/240 (49%), Gaps = 7/240 (2%)

Query: 266 IKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITN 325
           +K   G   + G+SL +  GE+  + G +G G++ L+K + G+ + D G I +  + +  
Sbjct: 14  VKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVAEQPVVM 73

Query: 326 QRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARE 385
             P     + +  + ++     L  E++VAENI L      P  ++G +D+ ++ +    
Sbjct: 74  SGPLDAKAKGIVFIHQEL---SLADELSVAENIYLGEL---PRKRFGLVDWAELEAKTNA 127

Query: 386 LMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKR 445
           ++E+  V G         LS  NQQ   IAR +  +   +I  +PT  L       + + 
Sbjct: 128 ILEKLKV-GFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 446 LIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNIN 505
           +   +++G  +  IS  ++EI  ++DRI+V+ DGQ QG V+   T ++ +  +M+G  ++
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 64/242 (26%), Positives = 114/242 (47%), Gaps = 24/242 (9%)

Query: 23  DKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLG 82
           + VN E+++GE+    G  GAG++ +   L GL  P+ G + + G    I SP  A   G
Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332

Query: 83  IGMVHQHFMLVDAFTVTENIILGNEVTKGINL----DLKT----AKKKILELSERYGLSV 134
           I +V +           + ++LG      + L    DLK     A    + + ++Y   +
Sbjct: 333 ISLVPED-------RKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKL 385

Query: 135 EPDA-----LIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLI 189
           +        L+ ++S G QQ++ I K L    ++LI DEPT  +      E+  ++++L 
Sbjct: 386 DIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLA 445

Query: 190 KEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEK 249
            +G ++I+I+ ++ E+  VADRI  +  G+ + T    + T + L   + G      TEK
Sbjct: 446 AQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLD----TEK 501

Query: 250 AA 251
            A
Sbjct: 502 VA 503


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: 636
Number of extensions: 33
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: 503
Length adjustment: 34
Effective length of query: 472
Effective length of database: 469
Effective search space:   221368
Effective search space used:   221368
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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