Alignments for a candidate for mcm-large in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Sinorhizobium medicae WSM419

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011969864.1 SMED_RS21215 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000017145.1:WP_011969864.1
          Length = 712

 Score =  791 bits (2044), Expect = 0.0
 Identities = 405/707 (57%), Positives = 517/707 (73%), Gaps = 9/707 (1%)

Query: 17  VPADAARRFEELAAK---AGTGE-AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVH 72
           +P    + +E LA K   AG     W T E I V  L+  D    M  L++  G  PF+ 
Sbjct: 1   MPDKTIKDWEALAEKELKAGPESLTWHTPEGIDVKPLYTSDDTSGMGDLNSLPGFEPFLR 60

Query: 73  GPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRV 132
           GP ATMYA RPWTIRQYAGFSTA+ SNAFYRRNLAAGQ+G+SVAFDL THRGYDSD+PRV
Sbjct: 61  GPRATMYAGRPWTIRQYAGFSTAEASNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRV 120

Query: 133 AGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQL 192
            GDVG AGVAIDS+ DM+ LF GIPLD++SVSMTMNGAV+PILA ++V  EEQGV  ++L
Sbjct: 121 EGDVGKAGVAIDSVEDMKILFDGIPLDRISVSMTMNGAVIPILASFIVAGEEQGVSRDKL 180

Query: 193 AGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATA 252
           +GTIQNDILKEFMVRNTYIYPP+PSMRI+++I  YT+  MPK+NSISISGYHMQEAGAT 
Sbjct: 181 SGTIQNDILKEFMVRNTYIYPPEPSMRIVADIIEYTAKEMPKFNSISISGYHMQEAGATL 240

Query: 253 DIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLV 312
             E+A+TLADG +Y+RA  + GLNVD FA RLSFF+ IGMNFFME AKLRAAR+LW +++
Sbjct: 241 VQELAFTLADGREYVRAALAKGLNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIM 300

Query: 313 HQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAI 372
            +F P+   S+ LRTH QTSG SL  QD YNN++RT  EAM+A  G TQSLHTNS DEA+
Sbjct: 301 KEFKPEKASSLMLRTHCQTSGVSLQEQDPYNNIIRTAFEAMSAVLGGTQSLHTNSFDEAM 360

Query: 373 ALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGG 432
           ALPTDFSARIARNTQL LQ E+G TRV+DP +GS YVE LT +LA KAW  I+EVE +GG
Sbjct: 361 ALPTDFSARIARNTQLILQHETGVTRVVDPLAGSYYVESLTNELAEKAWALIEEVEALGG 420

Query: 433 MAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQ 492
           M KA+  G+PK  IEEAA R QA +D G + ++GVN+YRLE+E P+D+L++DN+ V   Q
Sbjct: 421 MTKAVNAGLPKRLIEEAATRRQAAVDRGEEVIVGVNRYRLENEQPIDILQIDNAAVRTAQ 480

Query: 493 KAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDAL 552
             ++ + R  R+ +K+K ALD +   A     +    NLL   ++A RA ATVGE++DA+
Sbjct: 481 IKRIEETRRRRNSQKMKEALDTLADVA-----RSGKGNLLAAALEAARARATVGEITDAM 535

Query: 553 EKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDR 612
            + FG YTA    ++ +Y +  +  PE+      + E  +  G +P+I++AK+GQDGHDR
Sbjct: 536 REAFGDYTAVPEVVTDIYGRAFEGDPELGVLAGRLGEVTKRLGHKPKIMVAKLGQDGHDR 595

Query: 613 GQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKEL 672
           G KVIA+A+ D+GFDV  GPLFQTPEE A  A+  +V V+GVSSLA GH TL+P L + L
Sbjct: 596 GSKVIASAFGDIGFDVVAGPLFQTPEEAAELALAEEVTVLGVSSLAAGHKTLMPQLAEAL 655

Query: 673 DKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLV 719
            + GR DI++  GGVIP QD+  L ++G   ++ PGT + ++A +++
Sbjct: 656 KERGREDIILVCGGVIPRQDYAYLMENGVSAVFGPGTHVLDAARAIL 702


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: 1304
Number of extensions: 39
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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