Alignments for a candidate for mcm-large in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Rhizorhabdus wittichii RW1

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_012049093.1 SWIT_RS14630 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000016765.1:WP_012049093.1
          Length = 716

 Score =  766 bits (1979), Expect = 0.0
 Identities = 406/701 (57%), Positives = 503/701 (71%), Gaps = 10/701 (1%)

Query: 24  RFEELAAKAGTGE--AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAF 81
           R+E  AAK   G+   W T E I V  L+       +D      G  PF  G  A+MYA 
Sbjct: 10  RWEAAAAKEVKGKDLTWNTPEGIAVKPLYTAADVAGID--PGLPGFAPFTRGVRASMYAG 67

Query: 82  RPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGV 141
           RPWTIRQYAGFSTA+ESNAFY RNL AGQKGLSVAFDL THRGYDSD+PRV GDVG AGV
Sbjct: 68  RPWTIRQYAGFSTAEESNAFYHRNLKAGQKGLSVAFDLATHRGYDSDHPRVTGDVGKAGV 127

Query: 142 AIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDIL 201
           AID+I DM+ LF GIPLDQMSVSMTMNGAV+P+LA ++V  EEQGV   QL GTIQNDIL
Sbjct: 128 AIDTIDDMKILFDGIPLDQMSVSMTMNGAVIPVLAFFIVAGEEQGVPMAQLDGTIQNDIL 187

Query: 202 KEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLA 261
           KEFMVRNTYIYPP+PSMRIIS+IFA+TSANMPK+NSISISGYHMQEAGAT   E+A+T+A
Sbjct: 188 KEFMVRNTYIYPPEPSMRIISDIFAFTSANMPKFNSISISGYHMQEAGATQVQELAFTIA 247

Query: 262 DGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPK 321
           DG++Y++ G + GL++D+FA RLSFF+ IGMNFFME+AKLRAAR+LW +++ + G ++ +
Sbjct: 248 DGMEYVKYGVASGLDIDKFAGRLSFFFAIGMNFFMEIAKLRAARVLWHRVMTKLGARDER 307

Query: 322 SMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSAR 381
           S  LRTH QTSG SLT QD YNNV+RT IEAMAA  G TQSLHTN+LDEAIALPTDFSAR
Sbjct: 308 SKMLRTHCQTSGVSLTEQDPYNNVMRTTIEAMAAMLGGTQSLHTNALDEAIALPTDFSAR 367

Query: 382 IARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGI 441
           IARNTQ+ +Q+E+G T+V+DP  GS YVE LT +L  +AW  I++VE  GGMAKA+  G 
Sbjct: 368 IARNTQIVIQEETGMTKVVDPLGGSYYVESLTRELVDRAWEIIEKVEAEGGMAKAVAAGW 427

Query: 442 PKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRA 501
           PK  IEEA+A   ARID   + ++GVNKY+L  E P+D+L VDN  V   Q  ++  ++A
Sbjct: 428 PKAMIEEASAAKAARIDRVEEVIVGVNKYKLAQEDPIDILDVDNVAVREAQIRRIQAVKA 487

Query: 502 ERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTA 561
            RD    +AAL  +T  A          NLL L +D  RA AT+GE+S A+E VFGR+  
Sbjct: 488 GRDEATCQAALAALTEGA------QGSANLLALAVDCARAHATLGEISAAMEAVFGRFGT 541

Query: 562 QIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAY 621
               + G+Y     +        + VE   + +GR+PR+L+AKMGQDGHDRG  ++++A+
Sbjct: 542 NPTPVKGIYGGAYGDDRRWAGLVDGVETITRRKGRKPRMLVAKMGQDGHDRGANLVSSAF 601

Query: 622 ADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDIL 681
            DLGF+V  GPLFQTP+E A  A++ADV VVG SSLA GH TL+P L + L   GR DI 
Sbjct: 602 GDLGFEVVAGPLFQTPKEAAELALKADVDVVGASSLAAGHKTLIPELIQHLKDAGRGDIK 661

Query: 682 ITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722
           +  GGVIP QD+  LR  G   I+ PGT +  +A  +++ L
Sbjct: 662 VVAGGVIPAQDYQFLRDAGVQGIFGPGTNLVNAATEVLRLL 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: 1290
Number of extensions: 54
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: 716
Length adjustment: 40
Effective length of query: 688
Effective length of database: 676
Effective search space:   465088
Effective search space used:   465088
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 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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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 2024 update 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