GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Sinorhizobium meliloti 1021

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate SM_b20757 SM_b20757 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Smeli:SM_b20757
          Length = 712

 Score =  799 bits (2063), Expect = 0.0
 Identities = 402/681 (59%), Positives = 505/681 (74%), Gaps = 5/681 (0%)

Query: 35  GEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFST 94
           G  W T E I V  L+  D    +  L++  G  PFV GP ATMYA RPWT+RQYAGFST
Sbjct: 23  GLVWHTPEGIDVKPLYTSDDMSGIGHLNSLPGFEPFVRGPRATMYAGRPWTVRQYAGFST 82

Query: 95  AKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFA 154
           A+ SNAFYRRNLAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF 
Sbjct: 83  AEASNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVEDMKILFD 142

Query: 155 GIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPP 214
           GIPLD++SVSMTMNGAV+PILA ++V  EEQGV  ++L+GTIQNDILKEFMVRNTYIYPP
Sbjct: 143 GIPLDRISVSMTMNGAVIPILASFIVAGEEQGVSRDKLSGTIQNDILKEFMVRNTYIYPP 202

Query: 215 QPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVG 274
           +PSMRI+++I  YT+  MPK+NSISISGYHMQEAGAT   E+A+TLADG +Y+RA  + G
Sbjct: 203 EPSMRIVADIIEYTAKEMPKFNSISISGYHMQEAGATLVQELAFTLADGREYVRAALAKG 262

Query: 275 LNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGW 334
           LNVD FA RLSFF+ IGMNFFME AKLRAAR+LW +++ +F P+   S+ LRTH QTSG 
Sbjct: 263 LNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIMQEFKPEKASSLMLRTHCQTSGV 322

Query: 335 SLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQES 394
           SL  QD YNN+VRT  EAM+A  G TQSLHTNS DEA+ALPTDFSARIARNTQL LQ E+
Sbjct: 323 SLQEQDPYNNIVRTAFEAMSAVLGGTQSLHTNSFDEAMALPTDFSARIARNTQLILQHET 382

Query: 395 GTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQ 454
           G T+V+DP +GS YVE LT +LA KAWG I+EVE +GGM KA+  G+PK  IEEAA R Q
Sbjct: 383 GVTKVVDPLAGSYYVESLTNELAEKAWGLIEEVEALGGMTKAVNAGLPKRLIEEAATRRQ 442

Query: 455 ARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDK 514
           A +D   + ++GVNKYRLE+E P+D+L++DN+ V   Q  ++ + R  RD +K+K ALD 
Sbjct: 443 AAVDRAEEVIVGVNKYRLENEQPIDILQIDNAAVRTAQVKRIEETRRRRDSQKMKQALDA 502

Query: 515 ITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEV 574
           +   A     +    NLL   ++A RA ATVGE++DA+ + FG YTA    ++ +Y K  
Sbjct: 503 LADVA-----RSGKGNLLAAAVEAARARATVGEITDAMREAFGDYTAIPEVVTDIYGKAY 557

Query: 575 KNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLF 634
           +  PE+      + E  +  G +P+I++AK+GQDGHDRG KVIA+A+ D+GFDV  GPLF
Sbjct: 558 EGDPELGVLAGRLGEATKRLGHKPKIMVAKLGQDGHDRGAKVIASAFGDIGFDVVAGPLF 617

Query: 635 QTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFD 694
           QTPEE A  A+  +V V+GVSSLA GH TL+P L + L K G  DI++  GGVIP QD+D
Sbjct: 618 QTPEEAADLALAEEVTVIGVSSLAAGHRTLMPQLAEALKKRGGEDIIVVCGGVIPRQDYD 677

Query: 695 ELRKDGAVEIYTPGTVIPESA 715
            L ++G   ++ PGT + ++A
Sbjct: 678 YLMENGVAAVFGPGTQVLDAA 698


Lambda     K      H
   0.317    0.133    0.389 

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: 1293
Number of extensions: 40
Number of successful extensions: 2
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: 728
Length of database: 712
Length adjustment: 40
Effective length of query: 688
Effective length of database: 672
Effective search space:   462336
Effective search space used:   462336
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: 55 (25.8 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