GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Phaeobacter inhibens BS107

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Phaeo:GFF2770
          Length = 505

 Score =  253 bits (645), Expect = 1e-71
 Identities = 159/480 (33%), Positives = 259/480 (53%), Gaps = 13/480 (2%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P LS +G+ K +PGV A   +SFD  AG+VHAL+GENGAGKSTL+K++ G   P +G ++
Sbjct: 4   PLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKML 63

Query: 66  INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125
           ++G+  +  +   A   G+A+++Q   L   + VAENI LG    +     R L      
Sbjct: 64  LHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGM---ETPPALRDLATQIRK 120

Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185
           +  +  G+ +DP   +  LS G+ Q VEI + L ++ K++  DEPTS L+ +E++ LF+ 
Sbjct: 121 VS-ETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQT 179

Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245
           +++LR EG  ILY+SH++EEI  L D  T+ + G+ V      +    D + + MVG  +
Sbjct: 180 LQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARD-MAEMMVGTAL 238

Query: 246 GDIYGWQPRSYGEERLRLDAVKAPG------VRTPISLAVRSGEIVGLFGLVGAGRSELM 299
                   R+ G+  L +  +  P           + + VR GEI+G+ G+ G G+ EL+
Sbjct: 239 -QTPERSGRALGDVALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDELL 297

Query: 300 KGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINI-S 358
             + G T   A  V +D  PI    P      G++  PE+R      P  S+ +N  + +
Sbjct: 298 GVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAMLTA 357

Query: 359 ARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEM 418
           A R+ +     +  G  +  A+  I+S +++TPG E    +LSGGN QK ++GR + +  
Sbjct: 358 ATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQRP 417

Query: 419 KVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIA 478
            V+++++PT G+D  A   I   +  LAA G AV+  S DL E++ +AD    + EG ++
Sbjct: 418 DVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEGRLS 477



 Score = 63.9 bits (154), Expect = 1e-14
 Identities = 52/227 (22%), Positives = 106/227 (46%), Gaps = 21/227 (9%)

Query: 269 PGV--RTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPS 326
           PGV     +S  + +GE+  L G  GAG+S L+K ++G  +  +G++ +  +P    +P 
Sbjct: 16  PGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLLHGEPYTPGEPR 75

Query: 327 HAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386
            A A G+ +  +      +    +V +NI +       L            +    IR +
Sbjct: 76  QARADGIAMVFQHFS---LFDALNVAENIALGMETPPAL-----------RDLATQIRKV 121

Query: 387 NIKTPGAE----QLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVI 442
           + +T G      + + +LS G +Q+  + R L ++ K++++DEPT  +       ++  +
Sbjct: 122 S-ETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQTL 180

Query: 443 YALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADER 489
             L ++G ++L+ S  L E+  + D   ++R G+  GE +  +   R
Sbjct: 181 QKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSAR 227


Lambda     K      H
   0.319    0.136    0.391 

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: 610
Number of extensions: 33
Number of successful extensions: 7
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: 504
Length of database: 505
Length adjustment: 34
Effective length of query: 470
Effective length of database: 471
Effective search space:   221370
Effective search space used:   221370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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