GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Phaeobacter inhibens BS107

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  434 bits (1115), Expect = e-126
 Identities = 228/491 (46%), Positives = 322/491 (65%), Gaps = 2/491 (0%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           +L+L+GI K FPGV+AL G +L + PG V AL+GENGAGKST+MKVL GI+  D G ++ 
Sbjct: 7   VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
             +    +GP  ++  GI  IHQEL+L  +L++AENI+LG     RFG +DW  + A+ +
Sbjct: 67  AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
            +L KL + F +   VGDLSI +QQMVEIA+ L+ ++K +I DEPT +LTD E   LF V
Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           I +L+ QG GI YISHRM+EIF+I D ++V RDGQ+      A   E+++ +MM+GRKL+
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246

Query: 244 DQYPHLDKAPGDIRLKVDNL-CGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302
                     G++ L+V  L CG    DV+F +R+GE++G  GL+GAGRTE+ + L+G  
Sbjct: 247 LSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLR 306

Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362
             TSG + LDG EV   SP D +  GI  + EDRK  GLVLGM+ ++NM+L  +    +A
Sbjct: 307 NPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDL-KA 365

Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422
           G  +    E      +    +++TP  +Q +G LSGGNQQK+ I + L  RP VLI+DEP
Sbjct: 366 GPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEP 425

Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482
           TRG+DVG+K EI+ L+    A G ++I++SSEMPEVL ++DRI+ M+ G +   FT E+ 
Sbjct: 426 TRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEV 485

Query: 483 TQEVLMAAAVG 493
           T+E L+AA  G
Sbjct: 486 TEENLIAAISG 496



 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 73/234 (31%), Positives = 110/234 (47%), Gaps = 13/234 (5%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   + VS T+  GE+  + G  GAG++ LMKVL G      G + +    VV   P 
Sbjct: 18  PGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVAEQPVVMSGPL 77

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTAL--RYFSRAGGSLKHADEQQAVSDFIR 380
           D  A GIV+I ++     L   +SV EN+ L  L  + F     +   A     +     
Sbjct: 78  DAKAKGIVFIHQELS---LADELSVAENIYLGELPRKRFGLVDWAELEAKTNAILEKLKV 134

Query: 381 LFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440
            FN KT      +G LS  NQQ V IAR L    K +I DEPT  +    K  ++++I+ 
Sbjct: 135 GFNAKT-----RVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEVISD 189

Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            +  G+ I  +S  M E+  ++DRI V+ +G   G     +  +E +    +G+
Sbjct: 190 LQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGR 243



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 60/219 (27%), Positives = 106/219 (48%), Gaps = 5/219 (2%)

Query: 30  GRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPKSSQEAGIGIIHQELN 89
           G V+   G  GAG++ + + L G+    +G++   G E   T P  + E GI ++ ++  
Sbjct: 282 GEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRK 341

Query: 90  ---LIPQLTIAENIFLGREFVNRFGK-IDWKTMYAEADKLLAKLNLRFKSDK-LVGDLSI 144
              L+  +   +N+ L +    + G  +      A  D+   KL++R    K LVG+LS 
Sbjct: 342 GQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSG 401

Query: 145 GDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRGIVYISHRMKEI 204
           G+QQ + I K LS    V+I+DEPT  +       +  ++R+L +QG  ++ IS  M E+
Sbjct: 402 GNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEV 461

Query: 205 FEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
             + D +     G+ +       +TE++LI  + G   E
Sbjct: 462 LHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTE 500


Lambda     K      H
   0.318    0.137    0.380 

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: 674
Number of extensions: 37
Number of successful extensions: 7
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: 501
Length of database: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
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: 41 (21.7 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:

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