Alignments for a candidate for mcm-large in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Cereibacter sphaeroides ATCC 17029

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011840653.1 RSPH17029_RS04415 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000015985.1:WP_011840653.1
          Length = 709

 Score =  833 bits (2153), Expect = 0.0
 Identities = 431/706 (61%), Positives = 528/706 (74%), Gaps = 8/706 (1%)

Query: 20  DAARRF--EELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYAT 77
           DA R+   +EL  K+     W T E IPV  L+       M+ LD   G+ PF  G  AT
Sbjct: 6   DAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRAT 65

Query: 78  MYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVG 137
           MYA RPWTIRQYAGFSTA+ SNAFYR+ LAAGQ+G+SVAFDL THRGYDSD+PRV GDVG
Sbjct: 66  MYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVG 125

Query: 138 MAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQ 197
            AGVAIDSI DM+ LF GIPL+++SVSMTMNGAV+PILA ++VT EEQGV    L+GTIQ
Sbjct: 126 KAGVAIDSIEDMKILFDGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTIQ 185

Query: 198 NDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMA 257
           NDILKEFMVRNTYIYPP+PSMRII++I  YTS  MPK+NSISISGYHMQEAGA    E+A
Sbjct: 186 NDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQELA 245

Query: 258 YTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGP 317
           YTLADG +Y+RA  + G+NVD FA RLSFF+ IGMNFFME AKLRAAR+LW +++ +F P
Sbjct: 246 YTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSEFAP 305

Query: 318 KNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTD 377
           K P S+ LRTH QTSG SL  QD YNNV+RT  EAM+A  G TQSLHTN+LDEAIALPT+
Sbjct: 306 KKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPTE 365

Query: 378 FSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAI 437
           FSARIARNTQ+ LQ+E+G TRV+DP +GS YVE LT +LA KAW  I+EVE +GGM KA+
Sbjct: 366 FSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKAV 425

Query: 438 EKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLV 497
             G+PK+RIEE+AAR QA ID G   ++GVNKYRL  E P+++L +DN  V   Q A+L 
Sbjct: 426 ASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLK 485

Query: 498 KLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFG 557
           K+RA RD    +AALD++T  A          NLL+  +DA RA A+VGE+S A+EKVFG
Sbjct: 486 KMRATRDEAACQAALDELTRRAAE------GGNLLEAAVDASRARASVGEISMAMEKVFG 539

Query: 558 RYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVI 617
           R+ A+++T+SGVY    +      + +  VE F + EGRRPR+L+ KMGQDGHDRG KVI
Sbjct: 540 RHRAEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVI 599

Query: 618 ATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGR 677
           ATA+AD+GFDVDVG LFQTPEE A+ A++ DVHVVG+SSLA GH TL P L + L + G 
Sbjct: 600 ATAFADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGA 659

Query: 678 PDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLR 723
            +IL+  GGVIP+QD+D L++ G   I+ PGT IP +A  ++  +R
Sbjct: 660 GEILVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIR 705


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: 1311
Number of extensions: 44
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: 709
Length adjustment: 40
Effective length of query: 688
Effective length of database: 669
Effective search space:   460272
Effective search space used:   460272
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 Apr 10 2024. 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)
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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