GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609471
          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:

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