GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Escherichia coli BW25113

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 16996 b2917 methylmalonyl-CoA mutase (NCBI)

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Keio:16996
          Length = 714

 Score =  812 bits (2097), Expect = 0.0
 Identities = 414/680 (60%), Positives = 513/680 (75%), Gaps = 10/680 (1%)

Query: 39  ETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKES 98
           +TAE I +  L+ E    +++   T  G+PP+V GP ATMY  +PWTIRQYAGFSTAKES
Sbjct: 28  QTAEGIAIKPLYTEADLDNLEVTGTLPGLPPYVRGPRATMYTAQPWTIRQYAGFSTAKES 87

Query: 99  NAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPL 158
           NAFYRRNLAAGQKGLSVAFDL THRGYDSDNPRVAGDVG AGVAID++ DM+ LF  IPL
Sbjct: 88  NAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGVAIDTVEDMKVLFDQIPL 147

Query: 159 DQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSM 218
           D+MSVSMTMNGAVLP+LA Y+V AEEQGV P++L GTIQNDILKE++ RNTYIYPP+PSM
Sbjct: 148 DKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDILKEYLCRNTYIYPPKPSM 207

Query: 219 RIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVD 278
           RII++I A+ S NMP++N+ISISGYHM EAGA    ++A+TLADG++YI+A  S GL +D
Sbjct: 208 RIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLADGIEYIKAAISAGLKID 267

Query: 279 QFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTA 338
            FAPRLSFF+GIGM+ FM VA LRAAR LW++ V  FG ++PKS++LRTH QTSGWSLT 
Sbjct: 268 DFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEAVSGFGAQDPKSLALRTHCQTSGWSLTE 327

Query: 339 QDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTR 398
           QD YNNV+RT IEA+AAT G TQSLHTN+ DEA+ LPTDFSARIARNTQ+ +Q+ES   R
Sbjct: 328 QDPYNNVIRTTIEALAATLGGTQSLHTNAFDEALGLPTDFSARIARNTQIIIQEESELCR 387

Query: 399 VIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARID 458
            +DP +GS Y+E LT  + ++A   IQ++++ GGMAKAIE G+PK  IEEA+AR Q+ ID
Sbjct: 388 TVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMAKAIEAGLPKRMIEEASAREQSLID 447

Query: 459 SGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWA 518
            G++ ++GVNKY+L+HE   DVL++DN  V  EQ A L ++RA RD   V AAL+ +T A
Sbjct: 448 QGKRVIVGVNKYKLDHEDETDVLEIDNVMVRNEQIASLERIRATRDDAAVTAALNALTHA 507

Query: 519 AGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGV----YSKEV 574
           A +      + NLL   ++A R  AT+GE+SDALE  F RY    + ++GV    Y +  
Sbjct: 508 AQH------NENLLAAAVNAARVRATLGEISDALEVAFDRYLVPSQCVTGVIAQSYHQSE 561

Query: 575 KNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLF 634
           K+  E +      E+F    GRRPRIL+AKMGQDGHDRG KVIA+AY+DLGFDVD+ P+F
Sbjct: 562 KSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDRGAKVIASAYSDLGFDVDLSPMF 621

Query: 635 QTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFD 694
            TPEE AR AVE DVHVVG SSLA GH TL+P L + L K GR DI +  GGVIP QD+ 
Sbjct: 622 STPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEALKKWGREDICVVAGGVIPPQDYA 681

Query: 695 ELRKDGAVEIYTPGTVIPES 714
            L++ G   IY PGT + +S
Sbjct: 682 FLQERGVAAIYGPGTPMLDS 701


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: 1287
Number of extensions: 37
Number of successful extensions: 3
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: 714
Length adjustment: 40
Effective length of query: 688
Effective length of database: 674
Effective search space:   463712
Effective search space used:   463712
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