GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araG in Sinorhizobium meliloti 1021

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>lcl|FitnessBrowser__Smeli:SM_b20713 SM_b20713 sugar uptake ABC
           transporter ATP-binding protein
          Length = 513

 Score =  373 bits (958), Expect = e-108
 Identities = 198/489 (40%), Positives = 308/489 (62%), Gaps = 2/489 (0%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L+  G+ K FPGV AL D+ F    G VHALMGENGAGKSTL+KIL+G Y P  G V + 
Sbjct: 24  LTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLR 83

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLP-HKGGIVNRSLLNYEAGL 126
           G  +       AL  G+A+I+QEL+L+P MTVAENI++ + P ++ G V+   +      
Sbjct: 84  GAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTAK 143

Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
             + L +D+DP+  +++LS+   QMVEIAKA++  + ++  DEPTS+L+ RE+ +LF +I
Sbjct: 144 LFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEII 203

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246
           R+LR +G  I+Y++H+M E+F ++D  +VF+DG+Y+ T     +V  D +++ MVGR+I 
Sbjct: 204 RDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLS-NEVTRDDIIRMMVGREIT 262

Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306
            ++  +    G+  L +  +   GV   +S  VR+GEI+G+ GLVG+GRS + + +FG T
Sbjct: 263 QMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGVT 322

Query: 307 QITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLG 366
             ++G + ID + + I   + AI   M    EDRK  G + +  + +N+ I+  +   + 
Sbjct: 323 PASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFVK 382

Query: 367 GCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEP 426
              ++        +   R L +KTP  ++ + NLSGGNQQK ++GRWL    ++++LDEP
Sbjct: 383 RGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPRILILDEP 442

Query: 427 TRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQA 486
           TRGIDVGAK EI+ ++  LA  GVAV+  SS++PEVLG++DRI+VM EG + G L   +A
Sbjct: 443 TRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAEA 502

Query: 487 DERQALSLA 495
            + + + LA
Sbjct: 503 TQIKVMELA 511


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: 625
Number of extensions: 30
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 504
Length of database: 513
Length adjustment: 34
Effective length of query: 470
Effective length of database: 479
Effective search space:   225130
Effective search space used:   225130
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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