Alignments for a candidate for mcm-large in Methylocapsa aurea KYG T

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Methylocapsa aurea KYG T

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_051952997.1 DL86_RS08405 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000746085.1:WP_051952997.1
          Length = 738

 Score =  934 bits (2414), Expect = 0.0
 Identities = 478/727 (65%), Positives = 571/727 (78%), Gaps = 18/727 (2%)

Query: 1   MSTLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDW 60
           MS +P F  +    A  P+D      +LA     GE W T E + V  +++    + +DW
Sbjct: 1   MSRIPDFSDLSFAPAAGPSD------QLA-----GEDWATPEGVVVKPIYHSADLEGIDW 49

Query: 61  LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLP 120
           LDT+ G+PP++ GPY  MYA RPWTIRQYAGFST +ESNAFYRRNLAAGQKGLSVAFDLP
Sbjct: 50  LDTFPGLPPYLRGPYPLMYALRPWTIRQYAGFSTPEESNAFYRRNLAAGQKGLSVAFDLP 109

Query: 121 THRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVV 180
           THRGYDSD+PRVA DVGMAGVAIDSI DMR LF+GIPLD+MSVSMTMNGAVLPILALY+V
Sbjct: 110 THRGYDSDHPRVAADVGMAGVAIDSIDDMRMLFSGIPLDEMSVSMTMNGAVLPILALYIV 169

Query: 181 TAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISI 240
            AEEQG    +LAGTIQNDILKEFMVRNTYIYPP  S+RI S+IFA+T+ NMPK+NSISI
Sbjct: 170 AAEEQGAPLGKLAGTIQNDILKEFMVRNTYIYPPAASLRITSDIFAFTAQNMPKFNSISI 229

Query: 241 SGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAK 300
           SGYHMQEAGA+AD+E+AYTLADG++YIRAG   GL++DQFAPRLSFF+   MNFFME+AK
Sbjct: 230 SGYHMQEAGASADLELAYTLADGLEYIRAGLKAGLDIDQFAPRLSFFFATSMNFFMEIAK 289

Query: 301 LRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHT 360
           LRAAR+LWAKLV  F P N KS++LRTH+QTSGWSLTAQD +NN++RT IEAMAATQGHT
Sbjct: 290 LRAARLLWAKLVKGFNPANEKSLALRTHAQTSGWSLTAQDPFNNIIRTQIEAMAATQGHT 349

Query: 361 QSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKA 420
           QSLHTN+ DEA+ALP++FSAR+ARNTQLFLQQESGTTR+IDPW GS YVE LT +LA + 
Sbjct: 350 QSLHTNAFDEALALPSEFSARVARNTQLFLQQESGTTRIIDPWGGSFYVERLTAELAARV 409

Query: 421 WGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDV 480
             H+ E+E +GGMAKAIE G+PK RIEEAAARTQARIDSG Q +IGVN YR + E  + +
Sbjct: 410 ATHLDEIEALGGMAKAIEAGLPKRRIEEAAARTQARIDSGAQTVIGVNAYRPQSETEVAI 469

Query: 481 LKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGR 540
           LKVD + V   Q AKL +L+A R+P  V   LD +T  A          NLL L I+A R
Sbjct: 470 LKVDAAAVRTRQIAKLERLKAGREPALVAEKLDALTQGA------KTSANLLALAIEAAR 523

Query: 541 AMATVGEMSDALEKVFGRYTAQIRTISGVYSKEV-KNTPEVEEARELVEEFEQAEGRRPR 599
           A ATVGE+S ALEKVFGR+ A+I+ ISGVY+ E    +  +   + LV +F + +GRRPR
Sbjct: 524 AKATVGEISFALEKVFGRHRAEIQAISGVYAAEAGVGSATIAYIKRLVADFAENDGRRPR 583

Query: 600 ILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAG 659
           IL+AK+GQDGHDRGQKV+A+A +D GF V++GPLF TPEE ARQAVEA+VH++GVSSLA 
Sbjct: 584 ILVAKIGQDGHDRGQKVVASALSDFGFAVEIGPLFSTPEEAARQAVEANVHILGVSSLAA 643

Query: 660 GHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLV 719
           GHLTL+P LR  L++ GRPDI+I VGGVIP QDFD L + GA  I+ PGTVIPE+A  L+
Sbjct: 644 GHLTLIPQLRAALEREGRPDIMIVVGGVIPPQDFDALAEAGAAAIFPPGTVIPEAAARLI 703

Query: 720 KKLRASL 726
           + L   L
Sbjct: 704 ELLNGRL 710


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: 1433
Number of extensions: 43
Number of successful extensions: 4
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: 738
Length adjustment: 40
Effective length of query: 688
Effective length of database: 698
Effective search space:   480224
Effective search space used:   480224
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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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
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