Aligments for a candidate for mcm-large in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcm-large in Bacteroides thetaiotaomicron VPI-5482

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 351618 BT2090 methylmalonyl-CoA mutase large subunit (NCBI ptt file)

Query= BRENDA::P11653
         (728 letters)



>lcl|FitnessBrowser__Btheta:351618 BT2090 methylmalonyl-CoA mutase
           large subunit (NCBI ptt file)
          Length = 715

 Score =  905 bits (2339), Expect = 0.0
 Identities = 461/716 (64%), Positives = 555/716 (77%), Gaps = 9/716 (1%)

Query: 7   FDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAG 66
           F ++D+  A  PA+ A    E     G    W T E I V  ++ ++  + M+ L   AG
Sbjct: 5   FKNLDIYAAFQPANGA----EWQKANGISADWNTPEHIDVKPVYTKEDLEGMEHLGYAAG 60

Query: 67  IPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYD 126
           +PP++ GPY+ MY  RPWTIRQYAGFSTA+ESNAFYRRNLA+GQKGLSVAFDL THRGYD
Sbjct: 61  LPPYLRGPYSVMYTLRPWTIRQYAGFSTAEESNAFYRRNLASGQKGLSVAFDLATHRGYD 120

Query: 127 SDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQG 186
            D+ RV GDVG AGV+I S+ +M+ LF GIPL +MSVSMTMNGAVLPI+A Y+    EQG
Sbjct: 121 PDHERVVGDVGKAGVSICSLENMKVLFDGIPLSKMSVSMTMNGAVLPIMAFYINAGLEQG 180

Query: 187 VKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQ 246
            K E++AGTIQNDILKEFMVRNTYIYPP  SM+IIS+IF YTS  MPK+NSISISGYHMQ
Sbjct: 181 AKLEEMAGTIQNDILKEFMVRNTYIYPPAFSMKIISDIFEYTSQKMPKFNSISISGYHMQ 240

Query: 247 EAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARM 306
           EAGATADIE+AYTLADG++Y+RAG + G+++D FAPRLSFFW IG N FME+AK+RAARM
Sbjct: 241 EAGATADIELAYTLADGLEYLRAGTAAGIDIDAFAPRLSFFWAIGTNHFMEIAKMRAARM 300

Query: 307 LWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTN 366
           LWAK+V QF PKNPKS++LRTHSQTSGWSLT QD +NNV RTCIEAMAA  GHTQSLHTN
Sbjct: 301 LWAKIVKQFNPKNPKSLALRTHSQTSGWSLTEQDPFNNVGRTCIEAMAAALGHTQSLHTN 360

Query: 367 SLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQE 426
           +LDEAIALPTDFSARIARNTQ+++Q+E+   + +DPW GS YVE LT +LA KAW  I+E
Sbjct: 361 ALDEAIALPTDFSARIARNTQIYIQEETYICKNVDPWGGSYYVEALTNELAHKAWERIEE 420

Query: 427 VEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNS 486
           VEK+GGMAKAIE GIPKMRIEEAAARTQARIDSG Q ++GVNKYRLE E P+D+L++DN+
Sbjct: 421 VEKLGGMAKAIETGIPKMRIEEAAARTQARIDSGSQTIVGVNKYRLEKEAPIDILEIDNT 480

Query: 487 TVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVG 546
            V  EQ   L +L+  R+  +V  AL  IT        +    NLL+L ++A R  AT+G
Sbjct: 481 AVRLEQIENLKRLKEGRNQAEVDKALAAITECV-----ETGKGNLLELAVEAARVRATLG 535

Query: 547 EMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMG 606
           E+S A EKV GRY A IRTISGVYS E KN  + + A EL E+F + EGR+PRI++AKMG
Sbjct: 536 EISYACEKVVGRYKAIIRTISGVYSSESKNDGDFKRACELAEKFAKKEGRQPRIMVAKMG 595

Query: 607 QDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVP 666
           QDGHDRG KV+AT YAD GFDVD+GPLFQTP E AR+AVE DVHVVGVSSLA GH TL+P
Sbjct: 596 QDGHDRGAKVVATGYADCGFDVDMGPLFQTPAEAAREAVENDVHVVGVSSLAAGHKTLIP 655

Query: 667 ALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
            + +EL KLGR DI++  GGVIP QD+D L K G   I+ PGT + ++A  +++ L
Sbjct: 656 QIMEELKKLGREDIVVIAGGVIPAQDYDFLYKAGVAAIFGPGTPVAKAACQILEIL 711


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: 1384
Number of extensions: 51
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: 715
Length adjustment: 40
Effective length of query: 688
Effective length of database: 675
Effective search space:   464400
Effective search space used:   464400
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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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