GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Echinicola vietnamensis KMM 6221, DSM 17526

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Echvi_4683 Echvi_4683 Methylmalonyl-CoA mutase, N-terminal domain/subunit

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Cola:Echvi_4683
          Length = 685

 Score =  865 bits (2234), Expect = 0.0
 Identities = 419/658 (63%), Positives = 526/658 (79%), Gaps = 5/658 (0%)

Query: 65  AGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRG 124
           AGI PF+ GPY+TMY  RPWT+RQYAGFSTA+ SNAFY++NL AGQKGLSVAFDL THRG
Sbjct: 30  AGIAPFLRGPYSTMYLTRPWTLRQYAGFSTAEASNAFYKKNLEAGQKGLSVAFDLATHRG 89

Query: 125 YDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEE 184
           YDSD+PRV GDVG AGVAIDS+  M+ LF GIPLD+MSVSMTMNGAV+P++A Y+V AEE
Sbjct: 90  YDSDHPRVQGDVGKAGVAIDSVLGMKLLFDGIPLDKMSVSMTMNGAVIPVMAFYIVAAEE 149

Query: 185 QGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYH 244
           QGV  +QL GTIQNDILKEFMVRNTYIYPP+PS+RII++IFA+T+ NMP +NSISISGYH
Sbjct: 150 QGVPLDQLKGTIQNDILKEFMVRNTYIYPPEPSLRIIADIFAFTAKNMPAFNSISISGYH 209

Query: 245 MQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAA 304
           M EAGAT ++E+AYTLADG++Y+R G   GL +D FAPRLSFFWG+GM+ F E+AKLRA 
Sbjct: 210 MLEAGATPELELAYTLADGLEYVRTGLKAGLAIDDFAPRLSFFWGVGMDHFTEIAKLRAG 269

Query: 305 RMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLH 364
           R+LWAKL+ +F P +PKS+ LR H QTSGWSLT QD +NNV RT IEA+AA  GHTQSLH
Sbjct: 270 RLLWAKLMKEFRPTHPKSLKLRAHCQTSGWSLTEQDAFNNVARTTIEALAAVMGHTQSLH 329

Query: 365 TNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHI 424
           TN+ DEA ALPTDFSA IARNTQ+ L++E G  +V+DPW GS  +EELT DL +KAW H+
Sbjct: 330 TNAFDEAFALPTDFSASIARNTQVILREEYGLRKVVDPWGGSVLLEELTEDLVKKAWAHL 389

Query: 425 QEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVD 484
           QEVEK+GGMAKAIE G+PK  IEEAAAR QA++D G++ ++GVN++ ++ E   D+L+VD
Sbjct: 390 QEVEKMGGMAKAIEAGLPKQMIEEAAARRQAKVDQGKEIVVGVNRFLVDEEEDFDILEVD 449

Query: 485 NSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMAT 544
           N  VL +Q+A+L +L+ +RD   V  +L+ IT AA     K  + NLL+L ++A R  AT
Sbjct: 450 NEAVLKQQQARLSQLKNDRDAAAVARSLEAITQAA-----KSGEGNLLELSVEAARERAT 504

Query: 545 VGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAK 604
           +GE+S A+EKV+GR+ A+ + +SGVYS E  N    +EA  L   FE+ EGRRPRIL+AK
Sbjct: 505 LGEISMAMEKVYGRHRAKNQVVSGVYSSEAGNDELFKEALTLTARFEKLEGRRPRILIAK 564

Query: 605 MGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTL 664
           MGQDGHDRG KVIA+  AD+GFDVD+GPLFQTPEE A+QAVE DVH+VG SSLAGGH  L
Sbjct: 565 MGQDGHDRGAKVIASGMADMGFDVDIGPLFQTPEEVAKQAVENDVHLVGASSLAGGHKVL 624

Query: 665 VPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
           +P L   L+++GRPDIL+  GGVIP  D++ L++ G +E++ PGTV+ ++AI ++  L
Sbjct: 625 IPQLIIALEEMGRPDILVVAGGVIPPHDYEFLKEKGVLEVFGPGTVLTKAAIRIMSVL 682


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: 1286
Number of extensions: 50
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: 685
Length adjustment: 39
Effective length of query: 689
Effective length of database: 646
Effective search space:   445094
Effective search space used:   445094
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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