GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupA in Phaeobacter inhibens BS107

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>lcl|FitnessBrowser__Phaeo:GFF2770 PGA1_c28130 ABC transporter,
           ATP-binding protein
          Length = 505

 Score =  325 bits (833), Expect = 2e-93
 Identities = 182/501 (36%), Positives = 288/501 (57%), Gaps = 6/501 (1%)

Query: 1   MAQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG 60
           M Q ++ ++ +TK +   VAND ++ D+  GE+HALLGENGAGKSTL+ M+ GL++P SG
Sbjct: 1   MTQPLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSG 60

Query: 61  SIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQ 120
            + ++G   T   P ++   GI MV QHF L +A  V ENI LG E        L+    
Sbjct: 61  KMLLHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGMETPPA----LRDLAT 116

Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180
           +I+ +SE YGL +DP   + D+S G +QRVEI++ L +   +LI DEPT+VLTP E++ L
Sbjct: 117 QIRKVSETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEIL 176

Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240
              ++ L  EG SI+ I+HKL+EIR++ D  T++R GK++     S T+++D+AEMMVG 
Sbjct: 177 FQTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGT 236

Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGI-PAIKGLSLEVKAGEIIGIAGIDGNGQSE 299
           ++  T E++     +  L I  L V        A+K + + V+ GEI+G+ G+ GNGQ E
Sbjct: 237 ALQ-TPERSGRALGDVALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDE 295

Query: 300 LVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLAL 359
           L+  ++G     +  +T+ G  +  L       L +   PE+R       ++++ EN  L
Sbjct: 296 LLGVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAML 355

Query: 360 QTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDR 419
               +  L+  G L +    E    +++ FDVR       A+  SGGN QK +I REV +
Sbjct: 356 TAATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQ 415

Query: 420 DPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQ 479
            PD+L+V+QPT G+D  A   I + L+     G AV+ +S +LDE++ ++D  A +++G+
Sbjct: 416 RPDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEGR 475

Query: 480 IQGIVTPETTNKQELGILMAG 500
           +         +  E+G++M G
Sbjct: 476 LSAPRPTAGLSVDEIGLMMGG 496



 Score = 82.4 bits (202), Expect = 3e-20
 Identities = 65/238 (27%), Positives = 112/238 (47%), Gaps = 12/238 (5%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G+ A   +S ++ AGE+  + G +G G+S LV+ I GL K  SG + + G+  T    R+
Sbjct: 17  GVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLLHGEPYTPGEPRQ 76

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389
                +  V +      L   L +AEN+AL      P   +      K++E     +  +
Sbjct: 77  ARADGIAMVFQ---HFSLFDALNVAENIALGME-TPPALRDLATQIRKVSETYGLPLDPY 132

Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449
              G          S G +Q+  I R + +DP LLI+ +PT  L    +E + + L   R
Sbjct: 133 RTVG--------DLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQTLQKLR 184

Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIEREE 507
            EG ++L +S +L+EI  L D   ++  G+  G   P  T+ +++  +M G +++  E
Sbjct: 185 SEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGTALQTPE 242


Lambda     K      H
   0.315    0.135    0.363 

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: 564
Number of extensions: 19
Number of successful extensions: 6
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: 510
Length of database: 505
Length adjustment: 34
Effective length of query: 476
Effective length of database: 471
Effective search space:   224196
Effective search space used:   224196
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