GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Chryseobacterium arthrosphaerae CC-VM-7

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_065401015.1 BBI00_RS21385 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_001684965.1:WP_065401015.1
          Length = 707

 Score =  857 bits (2214), Expect = 0.0
 Identities = 430/672 (63%), Positives = 528/672 (78%), Gaps = 6/672 (0%)

Query: 56  KDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSV 115
           KD     T  GI P++ GPY+TMY  +PWTIRQYAGFSTA+ESNAFYRRNLAAGQKGLSV
Sbjct: 41  KDESLTQTSPGIEPYLRGPYSTMYVQKPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSV 100

Query: 116 AFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPIL 175
           AFDL THRGYDSD+ RV GDVG AGVAIDS+ DM+ LF  IPLDQ+SVSMTMNGAVLPIL
Sbjct: 101 AFDLATHRGYDSDHSRVVGDVGKAGVAIDSVEDMKILFNEIPLDQISVSMTMNGAVLPIL 160

Query: 176 ALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKW 235
           + Y+V AEEQGVK EQL+GTIQNDILKEFMVRNTYIYPP PSM+II++IF YTS N+PK+
Sbjct: 161 SFYIVAAEEQGVKQEQLSGTIQNDILKEFMVRNTYIYPPAPSMKIIADIFEYTSQNIPKF 220

Query: 236 NSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFF 295
           NSISISGYHMQEAGAT  +EMAYTLADG++Y+R G   G+NVD FAPRLSFFW IGMN F
Sbjct: 221 NSISISGYHMQEAGATPVLEMAYTLADGLEYVRTGIKAGMNVDDFAPRLSFFWAIGMNHF 280

Query: 296 MEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAA 355
           ME+AK+RAAR +WA L+ QF P+NPKS++LRTHSQTSGWSLT Q+ +NN+ RT IEA+++
Sbjct: 281 MEIAKMRAARYIWANLLKQFNPQNPKSLALRTHSQTSGWSLTEQEPFNNITRTAIEALSS 340

Query: 356 TQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWD 415
             G TQSLHTN+LDEAIALPTD+SA+IARNTQ+ LQQESG   V+DP  GS  VE LT  
Sbjct: 341 ALGGTQSLHTNALDEAIALPTDYSAKIARNTQIILQQESGICDVVDPMGGSNLVESLTQQ 400

Query: 416 LARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLE-H 474
           +  +A  +I EVE+ GGM KAIE GIPKMRIEEAAA+ QA+IDSG + +IGVN ++    
Sbjct: 401 MIEEAMRYIDEVEQEGGMTKAIEAGIPKMRIEEAAAKKQAKIDSGEEFIIGVNSFKSSLK 460

Query: 475 EPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKL 534
           +  +++L +DN+ V  +Q  +L  ++AER+ E V   L+ I  +A     K    NLL L
Sbjct: 461 QDAIEILDIDNTEVRRKQIERLNNIKAERNSEAVTQILNDIRESA-----KTGKGNLLAL 515

Query: 535 CIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAE 594
           CI+A R   T+GEMSDA+E+ FGRY A I+TISGVY+         E+A  L ++FE+ E
Sbjct: 516 CIEAARRRVTLGEMSDAMEETFGRYKANIKTISGVYAMNAGKNEYFEKALHLTQKFEEEE 575

Query: 595 GRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGV 654
           GRRPRI++AKMGQDGHDRG KV+ATA+AD+GFDVDV PLFQTPEE A+QA+E D+H++GV
Sbjct: 576 GRRPRIMVAKMGQDGHDRGAKVVATAFADMGFDVDVAPLFQTPEEVAKQAIENDIHILGV 635

Query: 655 SSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPES 714
           SSLA GH TLVP + +EL KLG  DI I VGGVIP+QD++ L  +GA  I+ PGT +P+ 
Sbjct: 636 SSLAAGHKTLVPQVVEELSKLGADDITIVVGGVIPQQDYEFLYANGADFIFGPGTNLPKC 695

Query: 715 AISLVKKLRASL 726
           A+ ++++L A +
Sbjct: 696 AVEILERLLAKI 707


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: 1272
Number of extensions: 38
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: 707
Length adjustment: 40
Effective length of query: 688
Effective length of database: 667
Effective search space:   458896
Effective search space used:   458896
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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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:

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:

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:

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:

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