Alignments for a candidate for mcm-large in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Algoriphagus machipongonensis PR1

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_008202643.1 ALPR1_RS17365 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000166275.1:WP_008202643.1
          Length = 706

 Score =  911 bits (2354), Expect = 0.0
 Identities = 450/685 (65%), Positives = 548/685 (80%), Gaps = 5/685 (0%)

Query: 38  WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKE 97
           WETAE+I V + F+     ++  +   AG  P++ GPY +MYA R WTIRQYAGFSTA+E
Sbjct: 24  WETAEKIEVPSEFDPKEIANLKHIHFIAGTAPYLRGPYRSMYAMRAWTIRQYAGFSTAEE 83

Query: 98  SNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIP 157
           SNAFYR+NL AGQKGLSVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF  IP
Sbjct: 84  SNAFYRKNLEAGQKGLSVAFDLATHRGYDSDHPRVLGDVGKAGVAIDSVEDMKILFDQIP 143

Query: 158 LDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPS 217
           LDQMSVSMTMNGAV+PILA Y+V AEEQGVKPEQL+GTIQNDILKEFMVRNTYIYPPQPS
Sbjct: 144 LDQMSVSMTMNGAVIPILAFYIVAAEEQGVKPEQLSGTIQNDILKEFMVRNTYIYPPQPS 203

Query: 218 MRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNV 277
           M+II++IF YTS ++PK+NSISISGYHMQEAGATADIE+AYTLADG +Y+R G   G+++
Sbjct: 204 MKIIADIFEYTSQHIPKFNSISISGYHMQEAGATADIELAYTLADGWEYLRTGVKAGMDI 263

Query: 278 DQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLT 337
           D FAPRLSFFW IGMN+FME+AK+RA RMLWAK+V +F PKNPKS++LRTH QTSGWSLT
Sbjct: 264 DDFAPRLSFFWAIGMNYFMEIAKMRAGRMLWAKIVQKFNPKNPKSLALRTHCQTSGWSLT 323

Query: 338 AQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTT 397
            QD +NNV RT +EA+AA  G TQSLHTNSLDEAIALPTDFSARIARNTQL LQ E+G T
Sbjct: 324 EQDPFNNVTRTAVEALAAAMGGTQSLHTNSLDEAIALPTDFSARIARNTQLVLQDETGIT 383

Query: 398 RVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARI 457
             +DPW GS YVE LT  L +KAWG I+EVE +GGMAKAIE G+PK+RIEEAAA+ QARI
Sbjct: 384 HAVDPWGGSHYVEYLTDQLVQKAWGLIEEVESLGGMAKAIESGVPKLRIEEAAAKKQARI 443

Query: 458 DSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITW 517
           DSG+  ++GVN+++++ E  ++V  VDN+ V   Q A+L  ++ +RD + V  +L  +T 
Sbjct: 444 DSGKDIIVGVNRFKVDGESEIEVRDVDNAEVRKSQIARLQAIKEKRDQQAVDKSLQALTD 503

Query: 518 AAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNT 577
           AA +        NLL L + A R  AT+GE+S ALE+VFGR+ A  ++I+GVYSKEV+N 
Sbjct: 504 AANSGKG-----NLLGLAVSAARNRATLGEISSALEEVFGRHKAHNKSITGVYSKEVENQ 558

Query: 578 PEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTP 637
              ++A  L  +FE+ EGRRPRI++AKMGQDGHDRG KVIAT +ADLGFDVD+GPLFQTP
Sbjct: 559 ESFKKALSLSNQFEELEGRRPRIMVAKMGQDGHDRGAKVIATGFADLGFDVDIGPLFQTP 618

Query: 638 EETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELR 697
           EE A QA+E DVH+VG SSLA GH TL+P L   LDKLGRPDI++  GGVIP +D+D L+
Sbjct: 619 EEVAEQAIENDVHIVGASSLAAGHKTLIPQLIGALDKLGRPDIMVVAGGVIPTKDYDFLK 678

Query: 698 KDGAVEIYTPGTVIPESAISLVKKL 722
             G  E++ PGTV+ E+AI +++KL
Sbjct: 679 DAGVAEVFGPGTVLSEAAIKILEKL 703


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: 1371
Number of extensions: 39
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: 706
Length adjustment: 40
Effective length of query: 688
Effective length of database: 666
Effective search space:   458208
Effective search space used:   458208
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.

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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