GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7024900
          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 (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