Alignments for a candidate for mcm-large in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Azospirillum brasilense Sp245

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS24250 AZOBR_RS24250 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__azobra:AZOBR_RS24250
          Length = 732

 Score =  998 bits (2581), Expect = 0.0
 Identities = 509/726 (70%), Positives = 592/726 (81%), Gaps = 9/726 (1%)

Query: 1   MSTLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEA---WETAEQIPVGTLFNEDVYKD 57
           M++LP F ++ L  A   A  A      AA+ GT  A   W T E + V  L+       
Sbjct: 1   MTSLPDFSTLPLDAAVSNASPAEWSRRFAAETGTDPATALWRTPEMLDVKPLYTAADLDG 60

Query: 58  MDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAF 117
           +D L    G+ PF+ GPY TMY  +PWT+RQYAGFSTA+ESNAFYRRNLAAGQKGLSVAF
Sbjct: 61  LDHLAAMPGMAPFLRGPYPTMYVDKPWTVRQYAGFSTAQESNAFYRRNLAAGQKGLSVAF 120

Query: 118 DLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILAL 177
           DL THRGYDSD+PRV GDVGMAGVAIDSI DM+ LF GIPLDQMSVSMTMNGAVLP+LA 
Sbjct: 121 DLATHRGYDSDHPRVTGDVGMAGVAIDSILDMKTLFDGIPLDQMSVSMTMNGAVLPVLAG 180

Query: 178 YVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNS 237
           Y+V AEEQGV  ++L+GTIQNDILKEFMVRNTYIYPP+PSMRIIS+IFA+TS +MPK+NS
Sbjct: 181 YIVAAEEQGVSADKLSGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAFTSQHMPKFNS 240

Query: 238 ISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFME 297
           ISISGYH+QEAGATAD+E+AYTLADGV+Y RAG + GL +DQFAPRLSFFW IGMNFFME
Sbjct: 241 ISISGYHLQEAGATADLELAYTLADGVEYARAGLAAGLTIDQFAPRLSFFWAIGMNFFME 300

Query: 298 VAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQ 357
           VAK+RA RMLWAKL+ +F PK+ KS+SLRTHSQTSGWSLTAQDV+NNV RTCIEAMA+TQ
Sbjct: 301 VAKMRAGRMLWAKLIKEFAPKSDKSLSLRTHSQTSGWSLTAQDVFNNVTRTCIEAMASTQ 360

Query: 358 GHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLA 417
           GHTQSLHTN+LDEA+ALPTDFSARIARNTQLFLQQESGT RVIDPW GS YVE LT +LA
Sbjct: 361 GHTQSLHTNALDEALALPTDFSARIARNTQLFLQQESGTCRVIDPWGGSYYVERLTRELA 420

Query: 418 RKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPP 477
            +AWGHI+EVE+ GGMAKAIE GIPKMR+EEAAARTQARIDSGRQ ++GVNKYRLE E  
Sbjct: 421 ARAWGHIREVEETGGMAKAIETGIPKMRVEEAAARTQARIDSGRQTVVGVNKYRLEQEEA 480

Query: 478 LDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCID 537
           ++VLKVDNS V A+Q A+L +LRAERDP + +  L+ +T AA   D      NLL L +D
Sbjct: 481 IEVLKVDNSAVRAQQIAQLERLRAERDPIRCRQTLEALTNAAAAGDG-----NLLALSVD 535

Query: 538 AGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEV-KNTPEVEEARELVEEFEQAEGR 596
           A RA ATVGE+SDALEKV+GR+ A+IRTI+G+Y+ EV + +  +   R LV EF + +GR
Sbjct: 536 AIRARATVGEISDALEKVYGRHKAEIRTITGIYAGEVGRQSDAIARVRALVAEFAERDGR 595

Query: 597 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSS 656
           RPRI++AKMGQDGHDRGQKVIATA+ADLGFDVDVGPLFQTPEE ARQAVE D H+VGVSS
Sbjct: 596 RPRIMVAKMGQDGHDRGQKVIATAFADLGFDVDVGPLFQTPEEAARQAVENDCHIVGVSS 655

Query: 657 LAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAI 716
           LA GHLTLVP L+ EL++ G  DILI VGGV+P QD+D L   GA  I+ PGTVI E+A+
Sbjct: 656 LAAGHLTLVPQLKAELERHGAGDILIVVGGVVPPQDYDALYAAGATAIFPPGTVISEAAV 715

Query: 717 SLVKKL 722
            L++ L
Sbjct: 716 DLLRIL 721


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: 1448
Number of extensions: 47
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: 728
Length of database: 732
Length adjustment: 40
Effective length of query: 688
Effective length of database: 692
Effective search space:   476096
Effective search space used:   476096
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