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

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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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, or view the source code.

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