GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Sinorhizobium meliloti 1021

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



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

 Score =  414 bits (1065), Expect = e-120
 Identities = 214/490 (43%), Positives = 323/490 (65%), Gaps = 3/490 (0%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L  + + K FPGV ALD V F +  G VH LMGENGAGKSTL+KIL G Y PD G V + 
Sbjct: 24  LTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLR 83

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP-NSLGWVNKREAKRFVRE 123
           G  +R  S   ++  GIA+IHQEL  +P +TVAEN+ + + P N  G+V+  E +R   +
Sbjct: 84  GAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTAK 143

Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183
             E + + LDP  ++R LS+A RQMVEI KA+   + V+ +DEPTS+L+ RE   LF+++
Sbjct: 144 LFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEII 203

Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243
           RDLR+    ++YI+H+M+E++E+ D  ++FRDG+ I +H + E VTRD I+  MVGREI+
Sbjct: 204 RDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNE-VTRDDIIRMMVGREIT 262

Query: 244 DIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGAD 303
            ++     P+G+V  + K +  + + +  SF+VR GEI+G  GLVG+GRS +   ++G  
Sbjct: 263 QMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGVT 322

Query: 304 HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRV 363
               G + +DGK + + SA +AIRH +    EDRK+ G + +  + EN+ I+  +     
Sbjct: 323 PASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFVK 382

Query: 364 GMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDE 423
             F+  ++     +   + L++KTP+ ++++  LSGGNQQK ++ RWL   + +++ILDE
Sbjct: 383 RGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLL-TNPRILILDE 441

Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483
           PTRGIDVGAK EI+ ++ +LA  G A++MISSE+PEVLG+SDRI+VM +GR++G L R +
Sbjct: 442 PTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAE 501

Query: 484 ATEQSVLSLA 493
           AT+  V+ LA
Sbjct: 502 ATQIKVMELA 511



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 66/256 (25%), Positives = 122/256 (47%), Gaps = 11/256 (4%)

Query: 250 ARPLGEVRFAAKGIE----GHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHK 305
           A P  E    A+G+     G        F+++RG +    G  GAG+S LM ++ G  + 
Sbjct: 16  AVPKSEYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYP 75

Query: 306 KGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGM 365
             GE+ L G  I+++S  +A+ +GI +     +E  ++   TV+ENI I  R    R G 
Sbjct: 76  DQGEVKLRGAGIRLKSPLDALENGIAMI---HQELNLMPFMTVAENIWIR-REPKNRFG- 130

Query: 366 FLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPT 425
           F+D  +      +  + LKI      + +R LS  N+Q   +++ ++  +  V+I+DEPT
Sbjct: 131 FVDHGEMRRMTAKLFERLKIDLDPEIE-VRHLSVANRQMVEIAKAVSY-ESDVLIMDEPT 188

Query: 426 RGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDAT 485
             +       ++ +I  L  +G  IV I+ ++ E+  ++D   V R G+  G     + T
Sbjct: 189 SALTEREVAHLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVT 248

Query: 486 EQSVLSLALPQSSTAL 501
              ++ + + +  T +
Sbjct: 249 RDDIIRMMVGREITQM 264


Lambda     K      H
   0.320    0.136    0.385 

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: 640
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: 512
Length of database: 513
Length adjustment: 35
Effective length of query: 477
Effective length of database: 478
Effective search space:   228006
Effective search space used:   228006
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 (21.8 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