GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gguA in Shewanella sp. ANA-3

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= TCDB::O05176
         (512 letters)



>lcl|FitnessBrowser__ANA3:7024900 Shewana3_2074 ABC transporter
           related (RefSeq)
          Length = 499

 Score =  307 bits (787), Expect = 5e-88
 Identities = 182/503 (36%), Positives = 302/503 (60%), Gaps = 13/503 (2%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           ILE++ I+K +PGVKALE+V+L++  GE+HAL+GENGAGKSTL+KV++G        G+I
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDM--GDI 61

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
            + G  ++F    D++  GI  ++QE+ LVP L++A+N+FLG E    G+I +++ +   
Sbjct: 62  LFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADA 121

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
           R +L +  L       ++D  +  QQL+ IA+ ++ S K+L+LDEPTASL+  + + L  
Sbjct: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           +L + + +G+  + ITH L++V +++D+ITVLR+G  +   +    E+ +  +I  M+GR
Sbjct: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIG--EYLTAELPQPKLIEAMLGR 239

Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQV---LHDINVTVRKGEVVGIAGLMGA 301
            L+++   +     E    V    A      D  V   +  +N+TV KG+ VG+AGL+G+
Sbjct: 240 SLQEQLVDKQ----EKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGS 295

Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361
           GR+E   +VFG       +G + + G+ +++S    AI AG+A   EDRK  G++   +I
Sbjct: 296 GRSEVCNAVFGLDLVD--SGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSI 353

Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421
             N  LA  A +     + + ++ ++A  F  +L+I +    +    LSGGNQQKV+L++
Sbjct: 354 RENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILAR 413

Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481
           WL   P +L+LDEPTRGID+GA  EI  +I  L  +G  +L+ SSE+ EL+   +++ V+
Sbjct: 414 WLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473

Query: 482 NEGRIVAELPKGEASQESIMRAI 504
            +   V EL   E + + +M+AI
Sbjct: 474 RDRYAVRELSGAELTSQHVMQAI 496



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 60/245 (24%), Positives = 114/245 (46%), Gaps = 11/245 (4%)

Query: 261 ILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRIT 320
           ILE+K  + ++   +    L D+++ +  GEV  + G  GAG++     + G     +  
Sbjct: 4   ILELKQISKHYPGVK---ALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQ--SKDM 58

Query: 321 GDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIID 380
           GD+L  G+P   +T   A  AG++ V ++   + LV N  +  N  L       +  +I 
Sbjct: 59  GDILFLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEP--RRLGLIH 113

Query: 381 DIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGID 440
             K    A    T+ ++    +     + S   QQ + +++ +  +  VL+LDEPT  +D
Sbjct: 114 FKKMYADARAVLTQFKL-DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLD 172

Query: 441 VGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESI 500
                 ++ I+NQL A G  ++ I+  + ++    DRI V+  G+ + E    E  Q  +
Sbjct: 173 AKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKL 232

Query: 501 MRAIM 505
           + A++
Sbjct: 233 IEAML 237


Lambda     K      H
   0.316    0.135    0.374 

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: 549
Number of extensions: 31
Number of successful extensions: 9
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: 499
Length adjustment: 34
Effective length of query: 478
Effective length of database: 465
Effective search space:   222270
Effective search space used:   222270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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