Aligments for a candidate for rbsA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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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Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources