GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_01038
          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.

Links

Downloads

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:

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:

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