GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:351618
          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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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