GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Pontibacillus litoralis JSM 072002

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_036834456.1 N784_RS09590 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000775615.1:WP_036834456.1
          Length = 1079

 Score =  310 bits (794), Expect = 2e-88
 Identities = 208/552 (37%), Positives = 313/552 (56%), Gaps = 43/552 (7%)

Query: 43   GFEIKRIYTPA--DLGEDWNYMEKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEE 100
            G +I ++  P   D G+   ++ +   PG +PFT GV+    +G   T RQ+AG  T + 
Sbjct: 532  GLQIPKVALPTYHDWGDRLLWVLRENIPGAFPFTAGVFPFKRKGEDPT-RQFAGEGTPDR 590

Query: 101  SNKRYKYLLSQGQTG--LSVAFDLPTQLGYDSDH-PLAEGEVGKVGVAIDSLWDMRILFD 157
            +N+R+ YL S+G+    LS AFD  T  G D D  P   G+VG+ GV+I +L DM+ L+ 
Sbjct: 591  TNRRFHYL-SEGEAAKRLSTAFDSVTLYGEDPDERPDIYGKVGESGVSICTLDDMQKLYA 649

Query: 158  GIPL--DKVSTSMTINSTAANLLAMYILVAEEQGVSQEK--------------------- 194
            G  L     S SMTIN  A  +LAM+   A +Q +   K                     
Sbjct: 650  GFDLCHPTTSVSMTINGPAPIILAMFFNTAIDQQIEMFKKQEGREPNQEERDRIKAETIS 709

Query: 195  -LRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAEN-VPKWNPISISGYHIREAG 252
             +RGTVQ DILKE   + T IF  + ++R+  DI  Y  ++ V  +  +SISGYHI EAG
Sbjct: 710  VVRGTVQADILKEDQGQNTCIFSTEFALRMMGDIQQYFIDHDVKNYYSVSISGYHIAEAG 769

Query: 253  ANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLW 311
            AN + ++AFTLA+G  YV+  + RGMD++KFAP LSFFF+  N    E     R ARR+W
Sbjct: 770  ANPITQLAFTLANGFTYVEYYLSRGMDINKFAPNLSFFFS--NGLDPEYTVIGRVARRIW 827

Query: 312  AYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNS 371
            A +M++ + A N RS  L++H QT+G +L AQ+ + N +R  +QAL A+     SLHTNS
Sbjct: 828  AIVMRDKYGA-NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALLAIQDNCNSLHTNS 886

Query: 372  YDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKI 431
            YDEA++ PTE+SVR A+  Q II  E G+    + L G++ +E LT  + E  L+  E++
Sbjct: 887  YDEAITTPTEESVRRAMAIQMIINKEFGLTKNENSLQGSFIVEELTHLVEEAVLQEFERM 946

Query: 432  QKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVDPSI 491
               GG++ A+ER Y + +I E +  Y+ +   G   I+GVN ++   P   E +      
Sbjct: 947  NDRGGVLGAMERQYQRGKIQEESLYYEGKKHSGDLPIIGVNTYLNPNPPSEEDIDSMELA 1006

Query: 492  REKQIERLKKLRSERD----NKKVQE-ALDKLRNAAEKEDENLMPYIIEAHRHLATLQEV 546
            R  Q E++ ++ S RD    N +V E AL +L+  A K++ N+   ++E  + +A+L ++
Sbjct: 1007 RASQEEKMHQIHSLRDFQERNAQVTENALQRLKQVA-KQNGNIFAELMETVK-VASLGQI 1064

Query: 547  TDVLREIWGEYR 558
            T+ L E+ G+YR
Sbjct: 1065 TNALYEVGGQYR 1076


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: 1195
Number of extensions: 62
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: 1079
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1038
Effective search space:   541836
Effective search space used:   541836
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.

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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