GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_607 Predicted
           L-arabinose ABC transport system, ATP-binding protein
          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 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