Alignments for a candidate for mcm-large in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Phaeobacter inhibens BS107

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate GFF2118 PGA1_c21510 methylmalonyl-CoA mutase BhbA

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Phaeo:GFF2118
          Length = 707

 Score =  832 bits (2150), Expect = 0.0
 Identities = 429/700 (61%), Positives = 522/700 (74%), Gaps = 6/700 (0%)

Query: 26  EELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWT 85
           +EL  +      W T E I V  L+ E   KD+  + T  G  PF  G  ATMYA RPWT
Sbjct: 14  KELRGRPLDALTWNTLEGIDVKPLYTEADTKDLPHMGTMPGFGPFTRGVKATMYAGRPWT 73

Query: 86  IRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDS 145
           IRQYAGFSTA+ESNAFYRRNLAAGQ+G+SVAFDL THRGYDSD+PRV GDVG AGVAIDS
Sbjct: 74  IRQYAGFSTAEESNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVMGDVGKAGVAIDS 133

Query: 146 IYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFM 205
           + DM+ LF GIPLDQ+SVSMTMNGAV+PILA ++V  EEQG     LAGTIQNDILKEFM
Sbjct: 134 VEDMKILFDGIPLDQVSVSMTMNGAVIPILASFIVAGEEQGHDKSLLAGTIQNDILKEFM 193

Query: 206 VRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVD 265
           VRNTYIYPP+PSMRIIS+I  YTS  MPK+NSISISGYHMQEAGA    E+AYTLADG +
Sbjct: 194 VRNTYIYPPEPSMRIISDIIEYTSNEMPKFNSISISGYHMQEAGANLVQELAYTLADGRE 253

Query: 266 YIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSL 325
           Y+RA    G++VD+FA RLSFF+ IGMNFFME+AKLRAAR LW +++  F  KN +S  L
Sbjct: 254 YVRAAMEAGMDVDKFAGRLSFFFAIGMNFFMEIAKLRAARTLWHRVMTDFDAKNDRSKML 313

Query: 326 RTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARN 385
           RTH QTSG SL  QD YNNV+RT  EAM+A  G TQSLHTN+LDEAIALPTDFSARIARN
Sbjct: 314 RTHCQTSGVSLQEQDPYNNVIRTAYEAMSAVLGGTQSLHTNALDEAIALPTDFSARIARN 373

Query: 386 TQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMR 445
           TQL LQ+E+G T V+DP +GS YVE LT +L  KAW  ++EVE++GGM KA+  G+PK+R
Sbjct: 374 TQLVLQEETGVTNVVDPLAGSYYVESLTNELIEKAWALMEEVEEMGGMTKAVASGMPKLR 433

Query: 446 IEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDP 505
           IEE+AAR QA ID G + ++GVNKYR E E P+D+L VDN  V   Q A+L  LRA+RD 
Sbjct: 434 IEESAARRQAMIDRGEEVIVGVNKYRKEKEDPIDILDVDNVAVRDSQIARLETLRADRDS 493

Query: 506 EKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRT 565
              +AALD +T  A          NLL   ++A RA A+VGE+S A+EK FGR++A+++T
Sbjct: 494 AACEAALDNLTRVA------KEGGNLLAAAVEAARARASVGEISMAMEKEFGRHSAEVKT 547

Query: 566 ISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLG 625
           ++GVY    +        ++ +E+F +AEGRRPR+L+ KMGQDGHDRG KVIATA+AD+G
Sbjct: 548 LAGVYGAAYEGDEGFAAIQKSIEDFAEAEGRRPRLLVVKMGQDGHDRGAKVIATAFADIG 607

Query: 626 FDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVG 685
           FDVDVGPLFQTP+E A+ A++ DVHVVG+SS A GH TL P L K L + G  DI++  G
Sbjct: 608 FDVDVGPLFQTPDEAAQDAIDNDVHVVGISSQAAGHKTLAPQLVKALKEQGAEDIIVICG 667

Query: 686 GVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRAS 725
           GVIP+QD+  L  +G   I+ PGT IPE+A  ++K +R S
Sbjct: 668 GVIPQQDYQFLYDNGVKAIFGPGTNIPEAAQDILKLIRQS 707


Lambda     K      H
   0.317    0.133    0.389 

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: 1302
Number of extensions: 38
Number of successful extensions: 2
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: 728
Length of database: 707
Length adjustment: 40
Effective length of query: 688
Effective length of database: 667
Effective search space:   458896
Effective search space used:   458896
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 17 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