Alignments for a candidate for mcm-large in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Xanthobacter autotrophicus Py2

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_041578178.1 XAUT_RS25450 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000017645.1:WP_041578178.1
          Length = 560

 Score =  582 bits (1501), Expect = e-170
 Identities = 289/556 (51%), Positives = 394/556 (70%), Gaps = 3/556 (0%)

Query: 9   LKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYMEKLGFP 68
           L  + ++ + WEET V  FL+K  ERKE+F T   F +KR+YT AD       +E +G P
Sbjct: 7   LANLDDDVRHWEETEVAAFLKKQKERKEQFFTLGDFPVKRVYTAADAAA--TPIEDIGLP 64

Query: 69  GEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGY 128
           G YPFTRG Y TMYR R WTMRQ AG+ T E++NKR+KYL+ QGQTG+S  FD+PT +GY
Sbjct: 65  GRYPFTRGPYPTMYRSRNWTMRQIAGFGTGEDTNKRFKYLIEQGQTGISTDFDMPTLMGY 124

Query: 129 DSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQ 188
           DSDHP+++GEVG+ GVAID+L DM  LFDGI L+K+S SMTIN +A  LLAMYI++A+++
Sbjct: 125 DSDHPMSDGEVGREGVAIDTLADMEALFDGIDLEKISVSMTINPSAWILLAMYIVLAQKR 184

Query: 189 GVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHI 248
           G   +KL GTVQ DILKEY+A+  YI+P  PS+R+  D I YCA+N+ ++NPI+ISGYHI
Sbjct: 185 GYDLDKLSGTVQADILKEYMAQKEYIYPIAPSVRIVRDCITYCAKNMKRYNPINISGYHI 244

Query: 249 REAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAAR 308
            EAG++ V EVAFTLA+ I YV+ V++ GM VD FAPRL+FFF    +F EEIAKFRA R
Sbjct: 245 SEAGSSPVDEVAFTLANLIVYVEEVLKTGMKVDDFAPRLAFFFVCQADFFEEIAKFRAVR 304

Query: 309 RLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLH 368
           R +A IMKE F A+NP SM LRFH QTA ++LT  Q   N+VR  +QALAAVLGG QSLH
Sbjct: 305 RCYAKIMKERFGARNPESMRLRFHCQTAAASLTKPQFMVNVVRTTLQALAAVLGGCQSLH 364

Query: 369 TNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYI 428
           TN +DEA ++PTE+++R+ALRTQQ+IA ES V   +DP+GG+YY+E LT    +  +  I
Sbjct: 365 TNGFDEAFAIPTEEAMRLALRTQQVIAEESNVTQVIDPVGGSYYVETLTTEYEKRIMDII 424

Query: 429 EKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPI-EVEILKV 487
            ++   GG ++ I+ G+ QK +A+ AY+     + G++ ++GVN  V +  + E+E+   
Sbjct: 425 SEVDARGGTIKLIQEGWFQKSVADFAYETALRKQSGEKPVIGVNTMVDESEVHEIELHPY 484

Query: 488 DPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVT 547
           D +  ++QI R +++R ERDN KV   LD+L   A+ E +N+MP  IE  R  AT+ ++ 
Sbjct: 485 DHTTADRQIARTQRVRRERDNVKVSALLDRLVEVAKDETQNIMPVTIELVREGATMGDIV 544

Query: 548 DVLREIWGEYRAPLIF 563
           + L+ +WG YR   +F
Sbjct: 545 ERLKTVWGVYRETPVF 560


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: 793
Number of extensions: 35
Number of successful extensions: 3
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources