Alignments for a candidate for mcm-large in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Dinoroseobacter shibae DFL-12

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 3607311 Dshi_0726 methylmalonyl-CoA mutase, large subunit (RefSeq)

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Dino:3607311
          Length = 712

 Score =  830 bits (2143), Expect = 0.0
 Identities = 428/704 (60%), Positives = 529/704 (75%), Gaps = 11/704 (1%)

Query: 27  ELAAKAGTGE-----AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAF 81
           +LAAK   G+      W+T E I V  L+  +  + +D L +  G  PF  G  ATMYA 
Sbjct: 10  DLAAKELRGKPLETLTWKTLEGIDVKPLYTAEDLEGLDHLGSVPGQAPFTRGVKATMYAG 69

Query: 82  RPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGV 141
           RPWTIRQYAGFSTA+ESNAFYR+ LAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGV
Sbjct: 70  RPWTIRQYAGFSTAEESNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVEGDVGKAGV 129

Query: 142 AIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDIL 201
           AIDS+ DM+ LF GIPLDQ+SVSMTMNGAV+PILA ++VT EEQG     L+GTIQNDIL
Sbjct: 130 AIDSVEDMKILFDGIPLDQVSVSMTMNGAVIPILANFIVTGEEQGHDRSVLSGTIQNDIL 189

Query: 202 KEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLA 261
           KEFMVRNTY+YPP+PSMRII++I  YTSA MPK+NSISISGYHMQEAGA    E+A+TLA
Sbjct: 190 KEFMVRNTYVYPPEPSMRIIADIIEYTSAEMPKFNSISISGYHMQEAGANLVQELAFTLA 249

Query: 262 DGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPK 321
           DG +Y+RA  + G++VD+FA RLSFF+ IGMNFFME AKLRAARMLW K++ +F PKNP+
Sbjct: 250 DGREYVRAAIARGMDVDKFAGRLSFFFAIGMNFFMEAAKLRAARMLWHKIMSEFEPKNPR 309

Query: 322 SMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSAR 381
           SM LRTH QTSG SL  QD YNNV+RT  EAM+A  G TQSLHTN+LDEAIALPT+FSAR
Sbjct: 310 SMMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAIALPTEFSAR 369

Query: 382 IARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGI 441
           IARNTQL LQ+E+G T V+DP +GS YVE LT +LA KAW  I+EVE++GGM KA+  G+
Sbjct: 370 IARNTQLILQEETGVTNVVDPLAGSYYVESLTNELAEKAWALIEEVEELGGMTKAVASGM 429

Query: 442 PKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRA 501
           PK+RIEE+AAR QA ID G + ++GVNKYR + E P+D+L++DN+ V   Q A+L K+RA
Sbjct: 430 PKLRIEESAARRQAMIDKGTEVIVGVNKYRKDKEDPIDILEIDNAKVRDGQVARLAKIRA 489

Query: 502 ERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTA 561
           ERD     +AL ++   A          NLL   ++A RA A+VGE+S A+EKVFGR+ A
Sbjct: 490 ERDEAACDSALAEVERCAAE------GGNLLAAAVEAARARASVGEISMAMEKVFGRHRA 543

Query: 562 QIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAY 621
           +++T++GVY    +        ++ VE+F   EGRRPR+L+ KMGQDGHDRG KVIATA+
Sbjct: 544 EVKTLAGVYGAAYEGDDGFAAIQKSVEDFAAEEGRRPRMLVVKMGQDGHDRGAKVIATAF 603

Query: 622 ADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDIL 681
           AD+GFDVDVGPLFQTPEE A+ A++ DVHV+G+SS A GH TL P L   L   G  DIL
Sbjct: 604 ADIGFDVDVGPLFQTPEEAAQDAIDNDVHVIGISSQAAGHKTLAPKLVDALKAQGAGDIL 663

Query: 682 ITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRAS 725
           +  GGVIP+QD+  L   G   I+ PGT IPE+A  +++ +R S
Sbjct: 664 VICGGVIPQQDYQYLYDRGVKAIFGPGTNIPEAAQDILRLIRES 707


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: 1308
Number of extensions: 42
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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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