GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Acidovorax sp. GW101-3H11

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_607
          Length = 517

 Score =  336 bits (862), Expect = 1e-96
 Identities = 190/487 (39%), Positives = 297/487 (60%), Gaps = 11/487 (2%)

Query: 4   STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63
           + P L   GI K F G+  L D+  + Y G++HALMG+NGAGKSTL+K+L+G    + G 
Sbjct: 15  AAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQ 74

Query: 64  VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPH----KGGIVNRSL 119
           + + GQ +      AA   G++ +YQE++L P ++VAENI+ G+ P     +G  ++ + 
Sbjct: 75  MRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWAT 134

Query: 120 LNYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREI 179
           L+  A   +  +G+ ID    L    +   Q+V IA+AL+  ++++  DEPTSSL   E+
Sbjct: 135 LHQRARDLVARIGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEV 194

Query: 180 DNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239
             LF V+R LR EG  I++V+H + +++A+SD ITV ++G +V  +   + +   AL+ A
Sbjct: 195 QKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWL-AKDLGPQALIAA 253

Query: 240 MVGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRT-----PISLAVRSGEIVGLFGLVGAG 294
           M+GRD+         +   +    + ++A G+       P+ L +R+GE+VGL GL+G+G
Sbjct: 254 MLGRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSG 313

Query: 295 RSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354
           R+EL + +FG  Q   G + ID Q +    P  AI  G+ LCPE+RK +GI+   SVR+N
Sbjct: 314 RTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVREN 373

Query: 355 INISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWL 414
           I ++ + +  +G   ++   +   A+ +++ L IKT   ++ I  LSGGNQQKAIL RW+
Sbjct: 374 IALALQARMGVGK-FLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWM 432

Query: 415 SEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMRE 474
           + E ++++LDEPTRGIDV AK EI + I  LA  G+AVLF SS++ EV+ VA RIVV+R+
Sbjct: 433 AIEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRD 492

Query: 475 GEIAGEL 481
               GEL
Sbjct: 493 RRKVGEL 499



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 65/227 (28%), Positives = 109/227 (48%), Gaps = 14/227 (6%)

Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334
           + L +  GEI  L G  GAG+S L+K + G  + + GQ+ +  Q +    P   +AA  +
Sbjct: 37  VQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAV---WPDSPLAAQRL 93

Query: 335 LCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTP--- 391
                 +   + P  SV +NI      +     C I  G+  + A  H R+ ++      
Sbjct: 94  GISTVYQEVNLCPNLSVAENIFAGRYPR-----CGIAQGFRIDWATLHQRARDLVARIGL 148

Query: 392 --GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQG 449
                +L+ +     QQ   + R LS E +V++LDEPT  +D     +++ V+  L ++G
Sbjct: 149 QIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSEG 208

Query: 450 VAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAM 496
           ++++F +  L +V  V+DRI V+R G   GE L +     QAL  AM
Sbjct: 209 LSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGP-QALIAAM 254


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: 604
Number of extensions: 33
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 469
Effective length of database: 482
Effective search space:   226058
Effective search space used:   226058
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