Alignments for a candidate for mcm-large in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Thauera aminoaromatica S2

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_004314665.1 C665_RS13530 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000310185.1:WP_004314665.1
          Length = 721

 Score =  845 bits (2184), Expect = 0.0
 Identities = 435/721 (60%), Positives = 541/721 (75%), Gaps = 11/721 (1%)

Query: 14  NAPV-PADAARRFEELAAKAGTGEA-----WETAEQIPVGTLFNEDVYKDMDWLDTYAGI 67
           N PV P      +++ AAK   G       W T E + V  L+ +   + +   DT  G 
Sbjct: 5   NDPVYPQPDIEAWKKAAAKQAPGGDLDKLNWITPEGLSVKPLYTKADTEGLQHADTLPGF 64

Query: 68  PPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDS 127
            PF+ GP  TMYA +PWTIRQYAGFSTA+ SNAFYR+ LAAG +G+SVAFDL THRGYDS
Sbjct: 65  EPFLRGPQPTMYAVKPWTIRQYAGFSTAEASNAFYRKALAAGGQGVSVAFDLATHRGYDS 124

Query: 128 DNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGV 187
           D+PRV GDVG AGVAIDS+ DM+ LF  IPLD++SVSMTMNGAVLPILA Y+V AEEQGV
Sbjct: 125 DHPRVTGDVGKAGVAIDSVEDMKILFDQIPLDKVSVSMTMNGAVLPILAGYIVAAEEQGV 184

Query: 188 KPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQE 247
             ++L+GTIQNDILKEFMVRNTYIYPP PSM+II++IF YT+ +MPK+NSISISGYH+QE
Sbjct: 185 SQDKLSGTIQNDILKEFMVRNTYIYPPTPSMKIIADIFGYTAQHMPKFNSISISGYHIQE 244

Query: 248 AGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARML 307
           AGA   IE+A+TLADGV+Y+R G + G++VD FA RLSFFW +GMNF++E+AK+RAAR+L
Sbjct: 245 AGANQAIELAFTLADGVEYVRTGINSGMDVDTFAGRLSFFWAVGMNFYLEIAKMRAARLL 304

Query: 308 WAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNS 367
           W +L+ QF PK+ KSM LRTHSQTSGWSLT QD YNNVVRT IEAMAA  G TQSLHTN+
Sbjct: 305 WWRLMKQFNPKSAKSMMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNA 364

Query: 368 LDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEV 427
           LDEAIALPT+FSARIARNTQ+ +Q+E+    V+DPW+GS  +E+LT D+A KAW  I+E+
Sbjct: 365 LDEAIALPTEFSARIARNTQIIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWALIEEI 424

Query: 428 EKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNST 487
           E +GGM +A+E G  KM++EE AA  QARIDSG+  ++GVNKY+L  E P+D+L +DN  
Sbjct: 425 ESMGGMTRAVESGWAKMKVEECAADKQARIDSGKDVIVGVNKYKLAKEDPIDILDIDNHA 484

Query: 488 VLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGE 547
           V   Q A+L K+RA RD   V+AAL  +T  A     +  + NLL L + A R  ATVGE
Sbjct: 485 VREAQIARLDKIRATRDTAAVQAALAALTKCA-----ETGEGNLLDLSVKAIRLRATVGE 539

Query: 548 MSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQ 607
           +SDALEKVFGRY A  + +SGVY   V+   + +  +  +E F   EGRRPR+++AK+GQ
Sbjct: 540 ISDALEKVFGRYRANPQAVSGVYGAVVEEQEDWKTLKADIEAFIAEEGRRPRVMIAKLGQ 599

Query: 608 DGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPA 667
           DGHDRG KV+A+A+ADLGFD+D+GPLFQTPEE AR AVE DVH VG SSLA GH TLVPA
Sbjct: 600 DGHDRGAKVVASAFADLGFDIDIGPLFQTPEEAARHAVENDVHAVGCSSLAAGHKTLVPA 659

Query: 668 LRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLD 727
           +  EL +LG  DI+  VGGVIP QD+D L   GA  I+ PGT IP +A  ++K++RA+  
Sbjct: 660 VIDELKRLGADDIITFVGGVIPAQDYDTLYAAGAKGIFGPGTPIPAAAREVLKQIRAARK 719

Query: 728 A 728
           A
Sbjct: 720 A 720


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: 1376
Number of extensions: 45
Number of successful extensions: 3
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: 721
Length adjustment: 40
Effective length of query: 688
Effective length of database: 681
Effective search space:   468528
Effective search space used:   468528
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
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