GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Paenisporosarcina indica PN2

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_075618392.1 GY23_RS06385 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_001939075.1:WP_075618392.1
          Length = 1086

 Score =  308 bits (789), Expect = 7e-88
 Identities = 208/552 (37%), Positives = 309/552 (55%), Gaps = 43/552 (7%)

Query: 43   GFEIKRIYTP--ADLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEE 100
            G +I R+  P   D GE   ++ K   PG +PFT GV+     G     RQ+AG  T E 
Sbjct: 539  GLKIPRVVLPKFVDYGEILRWVYKENVPGSFPFTAGVFPFKREGED-PKRQFAGEGTPER 597

Query: 101  SNKRYKYLLSQGQTG-LSVAFDLPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDG 158
            +N+R+ YL        LS AFD  T  G D D  P   G+VG+ GV+I +L DM+ L+DG
Sbjct: 598  TNRRFHYLSKDDNAKRLSTAFDSVTLYGEDPDTRPDIYGKVGESGVSICTLDDMKKLYDG 657

Query: 159  IPLDKVSTS--MTINSTAANLLAMYILVAEEQGV--SQEKL------------------- 195
              L   STS  MTIN  A  +LAM++  A +Q V  ++EKL                   
Sbjct: 658  FNLCAPSTSVSMTINGPAPIILAMFMNTAIDQQVKINEEKLGRTLTVEEFSEVRETTMQV 717

Query: 196  -RGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAGA 253
             RGTVQ DILKE   + T IF  + ++R+  DI  Y  +  V  +  +SISGYHI EAGA
Sbjct: 718  VRGTVQADILKEDQGQNTCIFSTEFALRMMGDIQQYFIDTKVRNYYSVSISGYHIAEAGA 777

Query: 254  NAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWA 312
            N + ++AFTL++G  YV+  + RGM++D FAP LSFFF+  N    E     R ARR+WA
Sbjct: 778  NPISQLAFTLSNGFTYVEYYLSRGMNIDDFAPNLSFFFS--NGLDPEYTVIGRVARRIWA 835

Query: 313  YIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSY 372
             +M++ + A N RS  L++H QT+G +L AQ+ + N +R  +QAL A+     SLHTN+Y
Sbjct: 836  VVMRDKYGA-NDRSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALMALQDNCNSLHTNAY 894

Query: 373  DEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQ 432
            DEA++ PTE+SVR A+  Q II  E G+    +PL GA+ +E +TD + E  L   ++I 
Sbjct: 895  DEAITTPTEESVRRAMAIQMIITKEHGLSKNENPLQGAFIVEEMTDLVEEAVLSEFDRIN 954

Query: 433  KMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP------IEVEILK 486
              GG++ A+E  Y + +I E +  Y+     G+  I+GVN ++   P        +EI +
Sbjct: 955  DRGGVLGAMETQYQRGKIQEESMHYEMLKHTGQLPIIGVNTYLNPNPPSAEDVDNMEIAR 1014

Query: 487  VDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEV 546
                 +E QI  L+  + ER++ + + AL +L+  A     N+   +++  + +A+L ++
Sbjct: 1015 ATIEEKESQILNLRAFQ-ERNSAESEAALKRLKEVA-VTGGNIFEQLMDTVK-VASLGQI 1071

Query: 547  TDVLREIWGEYR 558
            T+ L E+ G+YR
Sbjct: 1072 TNALYEVGGQYR 1083


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: 1278
Number of extensions: 69
Number of successful extensions: 8
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: 1086
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1045
Effective search space:   545490
Effective search space used:   545490
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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