GapMind for catabolism of small carbon sources

 

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

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate 3609471 Dshi_2855 methylmalonyl-CoA mutase, large subunit (RefSeq)

Query= BRENDA::O74009
         (563 letters)



>lcl|FitnessBrowser__Dino:3609471 Dshi_2855 methylmalonyl-CoA
           mutase, large subunit (RefSeq)
          Length = 657

 Score =  357 bits (917), Expect = e-103
 Identities = 210/489 (42%), Positives = 294/489 (60%), Gaps = 15/489 (3%)

Query: 83  RGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSDHPLAEGEVGKV 142
           + R W  R YAG++TAE SN  Y+  L++GQTGLSVAFDLPTQ GYDSDH L+ GEVGKV
Sbjct: 8   KDRPWLFRTYAGHSTAEASNALYRGNLAKGQTGLSVAFDLPTQTGYDSDHVLSRGEVGKV 67

Query: 143 GVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVSQEKLRGTVQND 202
           GV +  L DMR LF  IPLD+++TSMTIN+TA  LL++YI VAEEQG    KL+GTVQND
Sbjct: 68  GVPVAHLGDMRALFKDIPLDQMNTSMTINATAPWLLSLYIAVAEEQGADVTKLQGTVQND 127

Query: 203 ILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREAGANAVQEVAFT 262
           I+KEY++RGTYI PP+PS+R+ TD+  Y  E++PKWNP+++  YH++EAGA   QE+AF 
Sbjct: 128 IIKEYLSRGTYICPPKPSLRMITDVAAYTREHLPKWNPMNVCSYHLQEAGATPEQELAFA 187

Query: 263 LADG---IEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLWAYIMKEWF 319
           LA     ++ +K  +           R+SFF  A   F+ E+ K RA   LW  I ++ +
Sbjct: 188 LATATAVLDDLKGKVP-AEHFPAMVGRISFFVNAGIRFVTEMCKMRAFVTLWDEICRDRY 246

Query: 320 NAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVL---GGTQSLHTNSYDEAL 376
             ++P+    R+  Q     LT QQPENN+ R+ I+ LA  L      +++   +++EAL
Sbjct: 247 GVEDPKFRRFRYGVQVNSLGLTEQQPENNVYRILIEMLAVTLSKNARARAVQLPAWNEAL 306

Query: 377 SLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQKMGG 436
            LP     + +LR QQI+A E+ +++  D   G   ++     + E A   +  I  MGG
Sbjct: 307 GLPRPWDQQWSLRMQQIMALETDLLEFDDLFDGNPAVDRKVAELMEGARAELATIDGMGG 366

Query: 437 MMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP-----IEVEILKVDPSI 491
            + AIE  Y++  + EA       IE G+ ++VGVN +   EP      +  I+ VDP++
Sbjct: 367 AVAAIE--YMKSRLVEANSDRLGRIEGGETVVVGVNKYQQGEPSPLMDADGGIMVVDPAV 424

Query: 492 REKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLR 551
              QI RL+  R+ RD    Q+AL  LR AA     N+MP  I A +   T  E    +R
Sbjct: 425 EADQIARLQAWRAARDEDAAQKALADLREAA-LSGANVMPASIAAAKAGVTTGEWGLEIR 483

Query: 552 EIWGEYRAP 560
           + +GEYRAP
Sbjct: 484 KSFGEYRAP 492


Lambda     K      H
   0.318    0.134    0.388 

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: 820
Number of extensions: 40
Number of successful extensions: 6
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: 563
Length of database: 657
Length adjustment: 37
Effective length of query: 526
Effective length of database: 620
Effective search space:   326120
Effective search space used:   326120
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: 53 (25.0 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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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