GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Haloterrigena daqingensis JX313

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_076581961.1 BB347_RS05900 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_001971705.1:WP_076581961.1
          Length = 560

 Score =  673 bits (1737), Expect = 0.0
 Identities = 335/556 (60%), Positives = 435/556 (78%), Gaps = 3/556 (0%)

Query: 4   FDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFE-IKRIYTPADLGEDWNYM 62
           FD + L++I+  +  W E  V+  +++  ERKE F TD G + + R+YTPAD+  D +Y 
Sbjct: 2   FDPDDLEEIRAGKAEWHEEEVEPTVDRFGERKETFTTDTGGQTVDRLYTPADIS-DVDYQ 60

Query: 63  EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDL 122
           E LG+PGE P+TRGVY+T YRGR+WTMRQYAG++T E++N+RY YLL QGQTGLS+AFDL
Sbjct: 61  EDLGYPGEPPYTRGVYSTGYRGRLWTMRQYAGFSTPEDTNERYHYLLDQGQTGLSMAFDL 120

Query: 123 PTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYI 182
           PTQ+G+DSD  ++ GE+GK GVAIDSL DM  +FDGIPLD+VSTSMTIN+ A+ LLAMYI
Sbjct: 121 PTQMGHDSDASMSAGEIGKAGVAIDSLADMETVFDGIPLDEVSTSMTINAPASVLLAMYI 180

Query: 183 LVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPIS 242
            V ++QGV +E+LRGT+QNDILKEYIAR TYI+PP+ SMR+ TDI  +CA   PK+N IS
Sbjct: 181 AVGDQQGVDREQLRGTIQNDILKEYIARNTYIYPPESSMRIITDIFEFCASETPKFNTIS 240

Query: 243 ISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIA 302
           ISGYHIREAG+ A QE+AFTL DGIEYV+  IE G+DVD FAP+LSFFF  HNN  EE+A
Sbjct: 241 ISGYHIREAGSTAAQELAFTLGDGIEYVETAIEAGLDVDDFAPQLSFFFNGHNNIFEEVA 300

Query: 303 KFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLG 362
           KFRAARR+W  I+ E F+A +P+S  L+FHTQTAGS LTAQQ ENN+VRVA QALAAVLG
Sbjct: 301 KFRAARRMWHDIIDERFDANDPKSKQLKFHTQTAGSMLTAQQIENNVVRVAYQALAAVLG 360

Query: 363 GTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYE 422
           GTQSLHTN  DEAL+LPTE+SVR ALRTQQI+A+ESG  DT+DPL G+YY+E LTD + E
Sbjct: 361 GTQSLHTNGKDEALALPTEESVRTALRTQQILAHESGAADTIDPLAGSYYVESLTDDVEE 420

Query: 423 EALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEV 482
           EA + +E++ + GGM  AIE+ +VQ++I + ++  QKEI+   RIIVGVN F  DE  E+
Sbjct: 421 EAYEILEEVDERGGMREAIEQQWVQRQIQDTSFDRQKEIDSNDRIIVGVNEFEVDEDPEM 480

Query: 483 EILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLAT 542
           ++ ++    +++QI+ L+  R++RD+  V+  LD LR AA+ ED NLMPYII+A +  AT
Sbjct: 481 DVQEITEEDQQRQIDSLESTRADRDDDAVEAKLDALREAAQGED-NLMPYIIDAVKVYAT 539

Query: 543 LQEVTDVLREIWGEYR 558
           + E+ +VLR+ +GEY+
Sbjct: 540 VGEICNVLRDEFGEYQ 555


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: 858
Number of extensions: 27
Number of successful extensions: 4
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: 560
Length adjustment: 36
Effective length of query: 527
Effective length of database: 524
Effective search space:   276148
Effective search space used:   276148
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 24 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