GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacA in Azospirillum brasilense Sp245

Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate AZOBR_RS31645 AZOBR_RS31645 2-keto-gluconate dehydrogenase

Query= reanno::Pedo557:CA265_RS15345
         (567 letters)



>FitnessBrowser__azobra:AZOBR_RS31645
          Length = 523

 Score =  181 bits (460), Expect = 5e-50
 Identities = 161/571 (28%), Positives = 236/571 (41%), Gaps = 81/571 (14%)

Query: 17  IVIGSGISGGWAAKELTEKGLRVLMLERG--MNIEHITGYETAMKNPWDFKHAGKLTEEQ 74
           +++GSG  GG    +L  KG++ ++LE G   N+E     E A      F     L    
Sbjct: 14  VIVGSGAGGGTLGTQLALKGIKTVILEAGGRHNMEDFQNDEWA-----SFAQISWLDPRT 68

Query: 75  KRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKSLMWGRQSYRLSDH 134
                   RD+P   A   W V                    VGG ++ W   + R   H
Sbjct: 69  TSGSWRVSRDFPGLPA---WIVKA------------------VGGSTVHWAGAALRFQPH 107

Query: 135 NFEDNARDGHGS-----DWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMDL 189
            F+     G  +     DWP+   EL PWY  AE   G++ +            +P +  
Sbjct: 108 EFKTRTAYGEVAGANLLDWPITLEELEPWYAKAEDRMGVTRTNG----------IPGLPG 157

Query: 190 NIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKGRGNCQYRNLCSRGCPFGAYFSTQSS 249
           N   K +KA  ++    E     G +A  + P  GRG CQ    C +GC  GA +ST  +
Sbjct: 158 NNNFKVLKAGADKMGYTE--CHTGNMAINSEPRDGRGGCQQIGFCFQGCKSGAKWSTLIA 215

Query: 250 TLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVFVNGSTLG 309
            +P    T +L +R  + V  I +D   K   GV+  D +        A+IV V G+++ 
Sbjct: 216 EIPKGEETGKLEVRANAQVLKIEHDAKGK-VTGVVYADKD-GAIQRQKARIVAVAGNSIE 273

Query: 310 STFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRRANGIYIP 369
           S  +LLNS S   P+GL N SGQ+G N M H      +G   G  +K     R   +   
Sbjct: 274 SPRLLLNSASSMFPDGLANSSGQVGRNYMRH-----MTGSVYGVFEKPVRMYRGTTM--- 325

Query: 370 RYQNIGNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGKW----SMGLGG 425
               I  D+       G+ GG        ++  LS G         PG W    +  L G
Sbjct: 326 --AGIIRDEAKNKPDRGFVGGY-------EMETLSLGLPFMAAFLDPGAWGREFTSALDG 376

Query: 426 F---------GEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEM 476
           +         GE +P   N++ +   KKDK G PV  +  +   N+  MR         +
Sbjct: 377 YDHMAGMWLVGEDMPQESNRITLHADKKDKHGMPVPNVHFDDHPNDVAMRQHAYRQGMAL 436

Query: 477 LEKAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMP 536
            E  G    ++F    YP  + H +GT RM    +  V+NKW Q H+V N+FV+DGS   
Sbjct: 437 YESVGAT--RSFPTPPYP--STHNLGTNRMSEKARDGVVNKWGQTHDVANLFVSDGSQFT 492

Query: 537 SIACQNPSLTFMALTARACDYAVKELKKKNI 567
           +   +NP+LT +AL  R  DY   ++ K  I
Sbjct: 493 TGGAENPTLTIVALALRQADYIAGQMAKNAI 523


Lambda     K      H
   0.317    0.134    0.421 

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: 794
Number of extensions: 47
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: 567
Length of database: 523
Length adjustment: 35
Effective length of query: 532
Effective length of database: 488
Effective search space:   259616
Effective search space used:   259616
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 (21.7 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:

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