Alignments for a candidate for mcm-large in Sphingomonas indica Dd16

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Sphingomonas indica Dd16

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_085218115.1 B9N75_RS06775 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_900177405.1:WP_085218115.1
          Length = 714

 Score =  781 bits (2016), Expect = 0.0
 Identities = 416/700 (59%), Positives = 502/700 (71%), Gaps = 10/700 (1%)

Query: 25  FEELAAKAGTGE--AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFR 82
           +E LAAK   G    W T E I V  L+  +   D+D      G  PF  G  A+MYA R
Sbjct: 11  WEALAAKEVKGRDLTWHTPEGIAVKPLYTAEDVADID--PGLPGFAPFTRGVRASMYAGR 68

Query: 83  PWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVA 142
           PWTIRQYAGFSTA+ESNAFYRRNLAAGQKGLSVAFDL THRGYDSD+PRV GDVG AGVA
Sbjct: 69  PWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVTGDVGKAGVA 128

Query: 143 IDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILK 202
           IDS+ DM+ LF GIPLD+MSVSMTMNGAV+PILA ++V  EEQGV  E L GTIQNDILK
Sbjct: 129 IDSVEDMKILFDGIPLDKMSVSMTMNGAVIPILAFFIVAGEEQGVAQEMLDGTIQNDILK 188

Query: 203 EFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLAD 262
           EFMVRNTYIYPP+PSMRIIS+IFA+TSANMPK+NSISISGYHMQEAGAT   E+A+T+AD
Sbjct: 189 EFMVRNTYIYPPEPSMRIISDIFAFTSANMPKFNSISISGYHMQEAGATQVQELAFTIAD 248

Query: 263 GVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKS 322
           G++Y++ G + GL++D+FA RLSFF+ IGMNFFME+AKLRAAR+LW +++   G K+ +S
Sbjct: 249 GMEYVKYGVASGLDIDRFAGRLSFFFAIGMNFFMEIAKLRAARVLWYRVMTSLGAKDERS 308

Query: 323 MSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARI 382
             LRTH QTSG SLT QD YNNV+RT IEAMAA  G TQSLHTN+LDEAIALPTDFSARI
Sbjct: 309 KMLRTHCQTSGVSLTEQDPYNNVMRTTIEAMAAMLGGTQSLHTNALDEAIALPTDFSARI 368

Query: 383 ARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIP 442
           ARNTQL +Q+E+G T V+DP  GS YVE LT  L  +AW  I+ VE  GGMAKA+  G P
Sbjct: 369 ARNTQLVIQEETGMTNVVDPLGGSYYVEALTQRLVDEAWAIIERVEAEGGMAKAVAAGWP 428

Query: 443 KMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAE 502
           K  IEEAAA   ARID G Q ++GVN+YR   E P+++L VDN  V   Q  ++ K++AE
Sbjct: 429 KAMIEEAAAAAAARIDRGEQVIVGVNRYRKAEEDPIEILDVDNHAVREAQIRRIAKVKAE 488

Query: 503 RDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQ 562
           RD    ++AL  +   A        D NLL L ++  R  AT+GE+S A+E  FGRY   
Sbjct: 489 RDEAACQSALGALREGAKR------DGNLLALAVECARRRATLGEISSAMEDAFGRYGTN 542

Query: 563 IRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYA 622
              +SGVY              + VE   +  GR+PR+L+AKMGQDGHDRG  ++++ + 
Sbjct: 543 PAPVSGVYGGAYTGDARWTGLVDGVEMVGKRMGRKPRLLVAKMGQDGHDRGANLVSSMFG 602

Query: 623 DLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILI 682
           DLGF+V  GPLFQTP+E A  AVE  V VVG SSLA GH TLVP L   L  +GR DI +
Sbjct: 603 DLGFEVVPGPLFQTPKEAAALAVERQVDVVGASSLAAGHKTLVPELIGHLRDMGRADIKV 662

Query: 683 TVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
            VGGVIP QD+D LR+ G   I+ PGT + ++A  ++K L
Sbjct: 663 VVGGVIPAQDYDMLREAGVQGIFGPGTNLIDAAGEVLKLL 702


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: 1314
Number of extensions: 49
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 24 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