Alignments for a candidate for mcm-large in Prosthecochloris aestuarii DSM 271

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Prosthecochloris aestuarii DSM 271

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_012505457.1 PAES_RS04395 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000020625.1:WP_012505457.1
          Length = 1081

 Score =  894 bits (2310), Expect = 0.0
 Identities = 437/693 (63%), Positives = 548/693 (79%), Gaps = 5/693 (0%)

Query: 36   EAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTA 95
            + W T E I +   +  +   + + L    G+PPF  GPY +MY  RPWTIRQYAGFSTA
Sbjct: 394  QEWLTPEGIAIRNCYRANDSDNSEQLGFAPGLPPFNAGPYCSMYTVRPWTIRQYAGFSTA 453

Query: 96   KESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAG 155
            ++SN FYR+NLAAGQKGLSVAFDLPTHRGYDSD+PRV GDVG AGVAIDS+ DM+ LF G
Sbjct: 454  EKSNEFYRQNLAAGQKGLSVAFDLPTHRGYDSDHPRVVGDVGKAGVAIDSVEDMKILFDG 513

Query: 156  IPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQ 215
            IPLD MSVSMTMNGAVLPI+A Y+V AEEQGV+PEQL+GTIQNDILKEFMVRNTYIYPP 
Sbjct: 514  IPLDTMSVSMTMNGAVLPIMAFYIVAAEEQGVRPEQLSGTIQNDILKEFMVRNTYIYPPA 573

Query: 216  PSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGL 275
            PSMRII++IF YTS  MPK+NSISISGYHMQEAGATAD+E+AYTLADG++YIR G + GL
Sbjct: 574  PSMRIIADIFGYTSKMMPKFNSISISGYHMQEAGATADLELAYTLADGLEYIRTGLNAGL 633

Query: 276  NVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWS 335
             +D FAPRLSFFWGIGMNFFME+AKLRAARMLWAK+V +F PKNPKS+ LR+H QTSGWS
Sbjct: 634  AIDDFAPRLSFFWGIGMNFFMEIAKLRAARMLWAKIVKRFNPKNPKSLMLRSHCQTSGWS 693

Query: 336  LTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESG 395
            LT QD +NN+ RTCIEA+AA QGHTQSLHTN+LDEAIALP+ FSARIARNTQL+LQ+E+ 
Sbjct: 694  LTEQDPFNNITRTCIEALAAVQGHTQSLHTNALDEAIALPSVFSARIARNTQLYLQEETD 753

Query: 396  TTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQA 455
             TR IDPW GS YVE LT +LA KAW  I+E+E +GGM KAIE+G PKM IE+AA   QA
Sbjct: 754  ITRAIDPWGGSYYVESLTTELALKAWTIIEEIETMGGMVKAIEQGWPKMHIEKAATAKQA 813

Query: 456  RIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKI 515
            RID+G   ++G+N+Y  +++  LD L++DN+ VL +Q AKL K++ ERD +K   A++ +
Sbjct: 814  RIDTGEDIIVGINRYTPQNQTELDTLEIDNTEVLHQQLAKLEKVKKERDQQKTDKAIEAL 873

Query: 516  TWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVK 575
              AA     K+   NLL+L +DA R+ AT+GE+S ALE  FGRY + ++  + VY   + 
Sbjct: 874  RNAA-----KNGTGNLLELALDAARSRATLGEISSALEDAFGRYRSSVQLNANVYLAHMH 928

Query: 576  NTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQ 635
            +    ++A++L + F + EGRRPRIL+AK+GQDGHDRG KVIA  +AD+GFDVD+ PLFQ
Sbjct: 929  DNTAFKQAQDLADTFARHEGRRPRILVAKIGQDGHDRGAKVIAAGFADIGFDVDISPLFQ 988

Query: 636  TPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDE 695
            TPEE  RQA++ DVH++GVSSLAGGH TL+P++ K+L+K GR DI++  GGVIP +D++ 
Sbjct: 989  TPEEVVRQALDNDVHIIGVSSLAGGHKTLIPSVVKDLEKAGRRDIVVIAGGVIPHKDYEA 1048

Query: 696  LRKDGAVEIYTPGTVIPESAISLVKKLRASLDA 728
            L K G  +++ PGT+I E+A  +++ + A L+A
Sbjct: 1049 LYKAGIAKVFGPGTIIAEAACDILETMIAGLEA 1081



 Score = 61.6 bits (148), Expect = 2e-13
 Identities = 45/189 (23%), Positives = 80/189 (42%)

Query: 232 MPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIG 291
           +P++ +  +   +      T   E+A TL      +    S        A +       G
Sbjct: 167 LPQFRAFGLDSANSSMGELTPAKELAITLTGLERLLHDAASEQTTPRTIAAKTGVTLKAG 226

Query: 292 MNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIE 351
            +FF+ +AKLRA RMLW +++ + G  +   +      +    +    D +N ++    +
Sbjct: 227 RSFFLNIAKLRALRMLWPQILAEHGVDSDDQLEPHVTVRLDAAAPYRDDEHNALIILATQ 286

Query: 352 AMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEE 411
           A++   G   ++    L  A     D +  ++ N    L+ ES    V+DP  GSAY+E 
Sbjct: 287 AVSTIIGGCDTMIIPPLACASDHSPDITGHLSVNIHHMLRHESMLGHVLDPAGGSAYIET 346

Query: 412 LTWDLARKA 420
           LT  LA +A
Sbjct: 347 LTAKLAEEA 355


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: 1860
Number of extensions: 64
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 728
Length of database: 1081
Length adjustment: 43
Effective length of query: 685
Effective length of database: 1038
Effective search space:   711030
Effective search space used:   711030
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: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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:

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