Alignments for a candidate for mcm-large in Methylocella silvestris BL2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Methylocella silvestris BL2

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_049768223.1 MSIL_RS19215 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000021745.1:WP_049768223.1
          Length = 737

 Score =  902 bits (2331), Expect = 0.0
 Identities = 464/713 (65%), Positives = 555/713 (77%), Gaps = 12/713 (1%)

Query: 17  VPADAARRFEELAAKAGTGE------AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPF 70
           +P  A   F  +A KA   E      AW TAE + V   ++      +  +D++ G  P+
Sbjct: 4   IPDFAKIPFHSVATKAPAAEGERAEPAWLTAEGVAVKPAYSPQDRAGLSAVDSFPGHAPY 63

Query: 71  VHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNP 130
           + GPY TMY  +PWTIRQYAGFSTA++SNAFYRRNLAAGQ GLSVAFDL THRGYDSD+P
Sbjct: 64  LRGPYPTMYVNQPWTIRQYAGFSTAEDSNAFYRRNLAAGQMGLSVAFDLATHRGYDSDHP 123

Query: 131 RVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPE 190
           RVAGDVGMAGVAIDSIYDMR LF GIPLD+MSVSMTMNGAVLPILALY+V AEEQGVKPE
Sbjct: 124 RVAGDVGMAGVAIDSIYDMRTLFDGIPLDRMSVSMTMNGAVLPILALYIVAAEEQGVKPE 183

Query: 191 QLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGA 250
           QL GTIQNDILKEFMVRNTYIYPP PSMRI+S+IFAYTSA MPK+NSISISGYHMQEAGA
Sbjct: 184 QLQGTIQNDILKEFMVRNTYIYPPGPSMRIVSDIFAYTSARMPKFNSISISGYHMQEAGA 243

Query: 251 TADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAK 310
            AD+E+AYTLADGV+Y+RAG + GL++D FAPRLSFF+ IGMN FMEVAKLRAAR+LW++
Sbjct: 244 PADLELAYTLADGVEYVRAGLAAGLDIDAFAPRLSFFFAIGMNTFMEVAKLRAARLLWSQ 303

Query: 311 LVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDE 370
           L+ QF PK+ KS+ LRTH QTSGWSLTAQDV+NN +RT IEA+AA  G  QSLHTNSLDE
Sbjct: 304 LMAQFAPKSEKSLILRTHCQTSGWSLTAQDVFNNAMRTTIEALAAALGGAQSLHTNSLDE 363

Query: 371 AIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKV 430
           A+ALPTDFSARIARNTQ+ LQ ESG TR IDP  GS Y+E LT DLA +A  HI E+E +
Sbjct: 364 ALALPTDFSARIARNTQIMLQLESGITRTIDPLGGSYYLERLTADLAARAQSHIAEIETL 423

Query: 431 GGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLA 490
           GGM KAIE G+PK+RIEEAAA+TQA ID+G Q ++GVN+++ E E PL+V+KVDNS V A
Sbjct: 424 GGMTKAIEAGVPKLRIEEAAAKTQAHIDAGLQTVVGVNRFKPEREAPLEVMKVDNSVVRA 483

Query: 491 EQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSD 550
            Q AKL +LRAERD E V+ AL ++  AA +        NLL+L ++A RA ATVGE+S 
Sbjct: 484 AQIAKLERLRAERDAEGVERALARLKEAAASGTG-----NLLELGVEAARAKATVGEISA 538

Query: 551 ALEKVFGRYTAQIRTISGVYSKEVKNTPE-VEEARELVEEFEQAEGRRPRILLAKMGQDG 609
           ALE V+GR+ A  + ISGVY +E     E V    +L E F   EGR+PRIL+ K+GQDG
Sbjct: 539 ALESVYGRHAASTKVISGVYRREAGAANEAVHRVADLTEGFSHNEGRKPRILVVKLGQDG 598

Query: 610 HDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALR 669
           HDRGQKVIA+A++DLGFDV +GPLF TP E A QA++ +VH++GVSSLA GH+TL+P L+
Sbjct: 599 HDRGQKVIASAFSDLGFDVRIGPLFATPAEAAAQAIDEEVHIIGVSSLAAGHMTLLPELK 658

Query: 670 KELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
            EL+  GR DI++ VGGVIP  D D L   G   ++ PGTVIPE+A  L+ +L
Sbjct: 659 AELEARGRGDIMLVVGGVIPPADVDPLLDAGVAAVFLPGTVIPEAAERLINEL 711


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: 1368
Number of extensions: 54
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: 737
Length adjustment: 40
Effective length of query: 688
Effective length of database: 697
Effective search space:   479536
Effective search space used:   479536
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