GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mcm-large in Paraburkholderia bryophila 376MFSha3.1

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_01038 H281DRAFT_01038 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01038 H281DRAFT_01038
           methylmalonyl-CoA mutase
          Length = 703

 Score =  577 bits (1487), Expect = e-169
 Identities = 306/652 (46%), Positives = 426/652 (65%), Gaps = 7/652 (1%)

Query: 61  LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLP 120
           +D+  G  PFV GP+A+MY  +PWTIRQYAG++ A ++N  +R  LA G +GLSVAFDLP
Sbjct: 29  IDSMPGEAPFVRGPFASMYTQKPWTIRQYAGYAQASDTNLAFRTALAEGAQGLSVAFDLP 88

Query: 121 THRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVV 180
           T RGYDSD+P V+ DVGM GVAID++ DM  LF  I LD++SVSMTMNGAVLP+LA ++V
Sbjct: 89  TQRGYDSDDPAVSADVGMTGVAIDTVEDMTRLFEDIALDRVSVSMTMNGAVLPVLAAFIV 148

Query: 181 TAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISI 240
            AEE GV   QL GTIQNDILKEFMVRNT I+ P+PS+RI +++  Y   N+P++N++S+
Sbjct: 149 AAEESGVGASQLRGTIQNDILKEFMVRNTSIFAPEPSLRIAADVVEYLGKNVPRFNALSV 208

Query: 241 SGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAK 300
           SGYH QEAGA   +E+A T+A+   YI A    G+  D    R+SFF+G+GM+F++E+AK
Sbjct: 209 SGYHFQEAGADPVLELALTMANARKYITALAGRGMQADDVCQRMSFFFGVGMDFYVEIAK 268

Query: 301 LRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHT 360
           LRAAR+LWA +    G  + ++ +LR H QTSGWSLTAQ   NNVVRT +EA+AA  G T
Sbjct: 269 LRAARILWADIASASGATSDRARALRMHCQTSGWSLTAQKPMNNVVRTTVEALAAVFGGT 328

Query: 361 QSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKA 420
           QSLHTN  DEA++LP   ++R+AR+TQL LQ E+G   V+DPW+GS  +E+ T ++ +KA
Sbjct: 329 QSLHTNGYDEALSLPCADASRLARDTQLVLQHETGVCDVVDPWAGSYMMEKFTAEICQKA 388

Query: 421 WGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPL-D 479
              + E+E+ GG+   +E G  + +I  +A   QA I+S ++ ++GVN +    +  L +
Sbjct: 389 LTVMAEIERRGGVVDVVESGWVRDQIHRSALNIQAEIESRKRTVVGVNDFMTGCDEDLGE 448

Query: 480 VLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAG 539
              VD   V   Q  +L  ++A RDP +V+  LD +T AA     +  D NLL+L +   
Sbjct: 449 PQTVDGRRVRVLQTQRLAHIKARRDPTRVRNTLDALTRAA-----RGRDGNLLELTVACM 503

Query: 540 RAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPR 599
           RA ATVGE + ALE V+ RY   +  +   Y   +++  + ++    V +  +  GR PR
Sbjct: 504 RARATVGECTQALEAVWPRYQIGLPLLRDHYGANLESDKDWQDTCRAVADATKRLGRAPR 563

Query: 600 ILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAG 659
           +L+AK+GQDGHDRG ++IA A +D GF V  G +F +P +T + A    V V+GVSSLAG
Sbjct: 564 VLIAKLGQDGHDRGARIIAAALSDAGFAVFTGSMFASPSDTVQLAEGERVDVIGVSSLAG 623

Query: 660 GHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVI 711
               L+ AL  +L   G   I I VGG+I +     LR+ G    +  GT I
Sbjct: 624 AQNDLITALHDQLTVRGL-RIPIVVGGIIDQASQLVLRRSGVAACFPAGTPI 674


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: 1067
Number of extensions: 40
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: 703
Length adjustment: 39
Effective length of query: 689
Effective length of database: 664
Effective search space:   457496
Effective search space used:   457496
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.

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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:

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:

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:

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, or view the source code.

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