Alignments for a candidate for mcm-large in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Sphingomonas koreensis DSMZ 15582

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Ga0059261_3988 Ga0059261_3988 Methylmalonyl-CoA mutase, N-terminal domain/subunit

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Korea:Ga0059261_3988
          Length = 712

 Score =  772 bits (1993), Expect = 0.0
 Identities = 414/708 (58%), Positives = 503/708 (71%), Gaps = 12/708 (1%)

Query: 20  DAARRFEELAAKAGTGEAWETAEQIPVGTLFN-EDVYKDMDWLDTYAGIPPFVHGPYATM 78
           DA +   E   K G    W T E I V  L+  EDV  D        G  PF  G   +M
Sbjct: 8   DAWKALSEKEVK-GRDLTWRTPEGIDVKPLYTAEDVTADPG----LPGFAPFTRGVRGSM 62

Query: 79  YAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGM 138
           YA RPWTIRQYAGFSTA+ESNAFYRRNLAAGQKGLSVAFDL THRGYDSD+PRV GDVG 
Sbjct: 63  YAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVPGDVGK 122

Query: 139 AGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQN 198
           AGVAIDS+ DM+ LF GIPL +MSVSMTMNGAV+PILA ++V  EEQGV   QL GTIQN
Sbjct: 123 AGVAIDSVEDMKILFDGIPLGEMSVSMTMNGAVIPILAFFIVAGEEQGVPRAQLDGTIQN 182

Query: 199 DILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAY 258
           DILKEFMVRNTYIYPP+PSMRIIS+IF YTS  MPK+NSISISGYHMQEAGAT   E+A+
Sbjct: 183 DILKEFMVRNTYIYPPEPSMRIISDIFGYTSREMPKFNSISISGYHMQEAGATQVQELAF 242

Query: 259 TLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPK 318
           T+ADG++Y++ G + GL++D+FA RLSFF+ IGMNFFMEVAKLRAAR+LW +++ + G K
Sbjct: 243 TIADGMEYVKYGVASGLDIDKFAGRLSFFFAIGMNFFMEVAKLRAARVLWHRVMTKLGAK 302

Query: 319 NPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDF 378
           + +S  LRTH QTSG SLT QD YNNV+RT IEAMAA  G TQSLHTN+LDEAIALPTDF
Sbjct: 303 DERSKMLRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAMLGGTQSLHTNALDEAIALPTDF 362

Query: 379 SARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIE 438
           SARIARNTQ+ +Q+E+G T+V+DP  GS YVE LT +L  KAW  I+ VE  GGMAKA+ 
Sbjct: 363 SARIARNTQIVIQEETGMTKVVDPLGGSYYVEALTQELVDKAWEIIERVEAEGGMAKAVA 422

Query: 439 KGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVK 498
            G PK  IEEA+A T ARID G Q ++GVNKYR   E P+D+L VDN  V   Q A++ K
Sbjct: 423 AGWPKAMIEEASAATAARIDRGEQVIVGVNKYRKAEEDPIDILDVDNHAVREAQIARIKK 482

Query: 499 LRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGR 558
           +++ RD  K +AALD +   A   +      NLL L ++A R  AT+GE+S A+E VFGR
Sbjct: 483 VKSARDEAKCQAALDALREGARGTE------NLLALAVEAARHRATLGEISLAMEDVFGR 536

Query: 559 YTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIA 618
           +      +SGVY          E  ++ V   E+  GR+PR+L+AKMGQDGHDRG  +++
Sbjct: 537 HGTVPTPVSGVYGGAYAEDRRWERLKDGVAATERRLGRKPRMLVAKMGQDGHDRGANLVS 596

Query: 619 TAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRP 678
           +A+ DLGF+V  GPLFQTP+E A  A+  +V VVG SSLA GH TL+P +   L   GR 
Sbjct: 597 SAFGDLGFEVVPGPLFQTPQEAAELAIAENVDVVGASSLAAGHKTLIPQMIGHLKDAGRG 656

Query: 679 DILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASL 726
           DI +  GGVIP QD+  LR  G   I+ PGT +  +A  ++  L  +L
Sbjct: 657 DIKVIAGGVIPAQDYQFLRDAGVQAIFGPGTNLVNAAADVLTLLGHNL 704


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: 1317
Number of extensions: 52
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: 712
Length adjustment: 40
Effective length of query: 688
Effective length of database: 672
Effective search space:   462336
Effective search space used:   462336
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
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