Alignments for a candidate for mcmA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Sphingomonas koreensis DSMZ 15582

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

Query= SwissProt::Q3J4D7
         (709 letters)



>FitnessBrowser__Korea:Ga0059261_3988
          Length = 712

 Score =  974 bits (2518), Expect = 0.0
 Identities = 498/700 (71%), Positives = 576/700 (82%), Gaps = 6/700 (0%)

Query: 5   LDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRA 64
           LDAW+ L+EKE+KG+    LTW T EGI VKPLYT  D+       GLPG APFTRGVR 
Sbjct: 7   LDAWKALSEKEVKGRD---LTWRTPEGIDVKPLYTAEDVTADP---GLPGFAPFTRGVRG 60

Query: 65  TMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDV 124
           +MYAGRPWTIRQYAGFSTAE SNAFYR+ LAAGQ+G+SVAFDLATHRGYDSDHPRV GDV
Sbjct: 61  SMYAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVPGDV 120

Query: 125 GKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTI 184
           GKAGVAIDS+EDMKILF+GIPL ++SVSMTMNGAVIPILA FIV GEEQGVPRA L GTI
Sbjct: 121 GKAGVAIDSVEDMKILFDGIPLGEMSVSMTMNGAVIPILAFFIVAGEEQGVPRAQLDGTI 180

Query: 185 QNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQEL 244
           QNDILKEFMVRNTYIYPPEPSMRII+DI  YTS+EMPKFNSISISGYHMQEAGA  VQEL
Sbjct: 181 QNDILKEFMVRNTYIYPPEPSMRIISDIFGYTSREMPKFNSISISGYHMQEAGATQVQEL 240

Query: 245 AYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSEFA 304
           A+T+ADG EYV+  +A G+++D FAGRLSFFFAIGMNFFME AKLRAAR+LWHR+M++  
Sbjct: 241 AFTIADGMEYVKYGVASGLDIDKFAGRLSFFFAIGMNFFMEVAKLRAARVLWHRVMTKLG 300

Query: 305 PKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPT 364
            K   S MLRTHCQTSGVSL EQDPYNNVIRT  EAM+A LGGTQSLHTNALDEAIALPT
Sbjct: 301 AKDERSKMLRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAMLGGTQSLHTNALDEAIALPT 360

Query: 365 EFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKA 424
           +FSARIARNTQI++QEETG+T+VVDPL GSYYVE+LT EL +KAW +IE VEA GGM KA
Sbjct: 361 DFSARIARNTQIVIQEETGMTKVVDPLGGSYYVEALTQELVDKAWEIIERVEAEGGMAKA 420

Query: 425 VASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARL 484
           VA+G PK  IEE++A   A IDRGE VIVGVNKYR A+EDPI+ILD+DN AVR+AQIAR+
Sbjct: 421 VAAGWPKAMIEEASAATAARIDRGEQVIVGVNKYRKAEEDPIDILDVDNHAVREAQIARI 480

Query: 485 EKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGRHRAE 544
           +K+++ RDEA CQAALD L   A    NLL  AV+A+R RA++GEIS+AME VFGRH   
Sbjct: 481 KKVKSARDEAKCQAALDALREGARGTENLLALAVEAARHRATLGEISLAMEDVFGRHGTV 540

Query: 545 VKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFA 604
              +SGVYG AY  D  + +++  V +     GR+PRMLV KMGQDGHDRGA ++++AF 
Sbjct: 541 PTPVSGVYGGAYAEDRRWERLKDGVAATERRLGRKPRMLVAKMGQDGHDRGANLVSSAFG 600

Query: 605 DIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEILV 664
           D+GF+V  G LFQTP+EAA+ AI  +V VVG SSLAAGHKTL P++I  LK+ G G+I V
Sbjct: 601 DLGFEVVPGPLFQTPQEAAELAIAENVDVVGASSLAAGHKTLIPQMIGHLKDAGRGDIKV 660

Query: 665 ICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLI 704
           I GGVIP QDY FL+ AGV+AIFGPGTN+ +AA  +L L+
Sbjct: 661 IAGGVIPAQDYQFLRDAGVQAIFGPGTNLVNAAADVLTLL 700


Lambda     K      H
   0.318    0.133    0.377 

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: 1377
Number of extensions: 52
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: 709
Length of database: 712
Length adjustment: 39
Effective length of query: 670
Effective length of database: 673
Effective search space:   450910
Effective search space used:   450910
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:

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