Alignments for a candidate for mcm-large in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Klebsiella michiganensis M5al

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate BWI76_RS23935 BWI76_RS23935 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Koxy:BWI76_RS23935
          Length = 714

 Score =  798 bits (2061), Expect = 0.0
 Identities = 415/688 (60%), Positives = 506/688 (73%), Gaps = 10/688 (1%)

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

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

Query: 159 DQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSM 218
           D+MSVSMTMNGAVLP++A Y+V AEEQGV  EQL GTIQNDILKE++ RNTYIYPP+PSM
Sbjct: 148 DKMSVSMTMNGAVLPVMAFYIVAAEEQGVASEQLTGTIQNDILKEYLCRNTYIYPPKPSM 207

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

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

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

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

Query: 459 SGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWA 518
            G++ ++GVNKY+LE E    VL++DN  V  EQ A L K+RA+RD   VKAAL+ +T A
Sbjct: 448 QGKRVIVGVNKYKLEKEDETAVLEIDNVKVRNEQIASLEKIRAQRDDVTVKAALNALTHA 507

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

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

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

Query: 695 ELRKDGAVEIYTPGTVIPESAISLVKKL 722
            L+  G   IY PGT + ES   ++ ++
Sbjct: 682 FLQARGVAAIYGPGTPMLESVRDVLTRI 709


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: 1270
Number of extensions: 32
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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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
the source code
instructions for running GapMind on your computer

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