GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Paenisporosarcina indica PN2

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_075618030.1 GY23_RS04780 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_001939075.1:WP_075618030.1
          Length = 717

 Score =  921 bits (2380), Expect = 0.0
 Identities = 459/698 (65%), Positives = 567/698 (81%), Gaps = 6/698 (0%)

Query: 25  FEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPW 84
           F+E+A+ + T +++ T E I V + + ++  + ++ +    GI P   GPY TMY  RPW
Sbjct: 15  FQEVASTS-TRDSFLTNEGIHVSSRYGKEDAESLNHMSDLPGIAPNTRGPYPTMYVSRPW 73

Query: 85  TIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAID 144
           T+RQYAGFSTA+ESNAFYRRNLA GQKGLSVAFDL THRGYDSD+PRV GDVG AGVAID
Sbjct: 74  TVRQYAGFSTAEESNAFYRRNLAMGQKGLSVAFDLATHRGYDSDHPRVTGDVGKAGVAID 133

Query: 145 SIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEF 204
           SI DM+ LF GIPLDQMSVSMTMNGAVLPILA Y+VTAEEQGV  E+LAGTIQNDILKE+
Sbjct: 134 SIEDMKILFDGIPLDQMSVSMTMNGAVLPILAFYIVTAEEQGVSLEKLAGTIQNDILKEY 193

Query: 205 MVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGV 264
           MVRNTYIYPP+ SM+II++IF YTS +MPK+NSISISGYHMQEAGATADIE+AYTLADG+
Sbjct: 194 MVRNTYIYPPKMSMKIIADIFEYTSNHMPKFNSISISGYHMQEAGATADIELAYTLADGL 253

Query: 265 DYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMS 324
           +Y+R G   G+++D FAPRLSFFW IGMN+FMEVAK+RAAR +WA+++  F PKNPKS++
Sbjct: 254 EYVRTGLQAGIDIDSFAPRLSFFWAIGMNYFMEVAKMRAARRIWAQMMQTFDPKNPKSLA 313

Query: 325 LRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIAR 384
           LRTHSQTSGWSLT QD +NNV RT IEA AAT GHTQSLHTN+LDEAIALPTDFSARIAR
Sbjct: 314 LRTHSQTSGWSLTEQDPFNNVTRTLIEANAATMGHTQSLHTNALDEAIALPTDFSARIAR 373

Query: 385 NTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKM 444
           NTQLFLQ+E+  T+VIDPW GS  VE+LT +L +KAW  I+E+E++GGMAKAIE G+PKM
Sbjct: 374 NTQLFLQEETMMTKVIDPWGGSYAVEKLTDELMKKAWALIEEIEELGGMAKAIETGLPKM 433

Query: 445 RIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERD 504
           +IEEAAA+ QA+IDSG++ +IGVNK+RL+ E P+D+L +DNS V  +Q  ++  ++  R+
Sbjct: 434 KIEEAAAKKQAQIDSGKEIIIGVNKFRLQEEEPIDILNIDNSVVRQKQIERIETMKNMRN 493

Query: 505 PEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIR 564
            E V+ AL  +T AA     +  + NLL   + A R  AT+GE+SDA+EKV GR+ A IR
Sbjct: 494 EEAVQLALSALTKAA-----ESGEENLLACAVQAARVRATLGEISDAIEKVSGRHKAVIR 548

Query: 565 TISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADL 624
           ++SGVYS    N  E++  +++ E+F++ EGRRPRIL+AKMGQDGHDRG KVIATA+ADL
Sbjct: 549 SVSGVYSANFSNEEEIQTVKDMTEDFKENEGRRPRILIAKMGQDGHDRGAKVIATAFADL 608

Query: 625 GFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITV 684
           GFDVD+GPLFQTPEETARQA E DVHV+GVSSLA GH+TLVP L  EL K+GR DILI V
Sbjct: 609 GFDVDIGPLFQTPEETARQAAENDVHVIGVSSLAAGHMTLVPELLSELKKIGREDILIVV 668

Query: 685 GGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
           GGVIP QD+  LR++GA  I+ PGTVIP +A  +++++
Sbjct: 669 GGVIPAQDYAFLRENGASAIFGPGTVIPVAAAKVIEEI 706


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: 1295
Number of extensions: 40
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: 717
Length adjustment: 40
Effective length of query: 688
Effective length of database: 677
Effective search space:   465776
Effective search space used:   465776
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