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

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources