Alignments for a candidate for mcm-large in Azorhizobium caulinodans ORS 571

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Azorhizobium caulinodans ORS 571

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_043880187.1 AZC_RS09195 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000010525.1:WP_043880187.1
          Length = 718

 Score =  981 bits (2537), Expect = 0.0
 Identities = 506/717 (70%), Positives = 576/717 (80%), Gaps = 9/717 (1%)

Query: 12  LGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFV 71
           +   P  AD   R  ELA  A     W T E IPV  L+       + ++DTY GI PF+
Sbjct: 1   MSRLPAFADIEWRAPELAPPADAPAPWLTPEGIPVKGLYGPADIAGLSFIDTYPGIAPFL 60

Query: 72  HGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPR 131
            GPY TMYA +PWTIRQYAGFSTA++SNAFYRRNLAAGQKGLSVAFDL THRGYDSD+PR
Sbjct: 61  RGPYPTMYATQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPR 120

Query: 132 VAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQ 191
           VAGDVGMAGVAIDSIYDMR LF+GIPLDQMSVSMTMNGAVLPILAL+VV AEEQGV   +
Sbjct: 121 VAGDVGMAGVAIDSIYDMRTLFSGIPLDQMSVSMTMNGAVLPILALFVVAAEEQGVPAAK 180

Query: 192 LAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGAT 251
           L+GTIQNDILKEFMVRNTYIYPP PSMRIIS+IFA TS  MP++NSISISGYHMQEAGAT
Sbjct: 181 LSGTIQNDILKEFMVRNTYIYPPAPSMRIISDIFALTSKEMPRFNSISISGYHMQEAGAT 240

Query: 252 ADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKL 311
            D+E+AYTLADGV+Y+RAG   GL +D FAPRLSFFW IGMNFFMEVAKLRAAR+LW +L
Sbjct: 241 QDLELAYTLADGVEYVRAGAKAGLPIDAFAPRLSFFWAIGMNFFMEVAKLRAARLLWTRL 300

Query: 312 VHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEA 371
           +   G KNPKS+ LRTHSQTSGWSLTAQDV+NNV+RT +EAMAATQGHTQSLHTN+LDEA
Sbjct: 301 MSDLGAKNPKSLPLRTHSQTSGWSLTAQDVFNNVIRTMVEAMAATQGHTQSLHTNALDEA 360

Query: 372 IALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVG 431
           +ALPTDFSARIARNTQ+ LQQESGTTR IDPW GS +VE LT DLA KAW HIQEVE +G
Sbjct: 361 LALPTDFSARIARNTQILLQQESGTTRQIDPWGGSFFVERLTADLAAKAWDHIQEVEALG 420

Query: 432 GMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAE 491
           GMAKAIE GIPK+RIEEAAA TQARID G Q ++GVNK++ E E P+DVLKVDNS V A 
Sbjct: 421 GMAKAIEAGIPKLRIEEAAATTQARIDGGAQIVVGVNKFKPERETPIDVLKVDNSAVRAA 480

Query: 492 QKAKLVKLRAERDPEKVKAALDKIT-WAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSD 550
           Q  KL +L+AERDP+ V AAL+ +T  A GN        NLL L IDA RA ATVGE+SD
Sbjct: 481 QIEKLRRLKAERDPQGVAAALEALTNGARGN-------GNLLALAIDAARAKATVGEISD 533

Query: 551 ALEKVFGRYTAQIRTISGVYSKEV-KNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDG 609
           ALE VFGR+ A+IR ISGVY +E    T +V + + L E FE  EGRRPRIL+AK+GQDG
Sbjct: 534 ALEAVFGRHRAEIRAISGVYKREAGAMTDKVAQVQRLTEAFEHNEGRRPRILVAKVGQDG 593

Query: 610 HDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALR 669
           HDRGQKVIA+A+ADLGFDVD+GPLF TPEE ARQAVE DVHVVG+SSLA GHLTLVPAL+
Sbjct: 594 HDRGQKVIASAFADLGFDVDIGPLFATPEEAARQAVENDVHVVGISSLAAGHLTLVPALK 653

Query: 670 KELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASL 726
             L+  GR DI++ VGGV+P QD++ L+  GA  I+ PGTVI ++A  L+  L   L
Sbjct: 654 AALEAEGRGDIMVVVGGVVPPQDYEALKAAGAEAIFPPGTVIADAARDLLATLSTRL 710


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: 1453
Number of extensions: 49
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: 728
Length of database: 718
Length adjustment: 40
Effective length of query: 688
Effective length of database: 678
Effective search space:   466464
Effective search space used:   466464
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.

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