GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Caulobacter crescentus NA1000

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate CCNA_02459 CCNA_02459 methylmalonyl-CoA mutase alpha subunit

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__Caulo:CCNA_02459
          Length = 714

 Score =  984 bits (2543), Expect = 0.0
 Identities = 500/727 (68%), Positives = 578/727 (79%), Gaps = 19/727 (2%)

Query: 1   MSTLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDW 60
           MST P F  +     P PA            A  GEAW T E + V   F+      +D+
Sbjct: 1   MSTFPDFTKIAFAEVPAPA------------APKGEAWNTPEGVAVAPAFDASDVAGLDF 48

Query: 61  LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLP 120
              + G+ PFV GPY TMY   PWT+RQYAGFSTA++SNAFYRRNLAAGQ GLSVAFDL 
Sbjct: 49  TGGFPGVAPFVRGPYPTMYVTNPWTVRQYAGFSTAEDSNAFYRRNLAAGQMGLSVAFDLA 108

Query: 121 THRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVV 180
           THRGYDSD+ RV GDVGMAGVAIDSI DMR LF+GIPLD+MSVSMTMNGAVLPILALY+V
Sbjct: 109 THRGYDSDHERVKGDVGMAGVAIDSILDMRTLFSGIPLDKMSVSMTMNGAVLPILALYIV 168

Query: 181 TAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISI 240
            AEEQGV P++L+GTIQNDILKEFMVRNTYIYPP PSMRIIS+IFA+TSANMPK+NSISI
Sbjct: 169 AAEEQGVSPDKLSGTIQNDILKEFMVRNTYIYPPAPSMRIISDIFAFTSANMPKFNSISI 228

Query: 241 SGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAK 300
           SGYHMQEAGATAD+E+AYTLADGV+Y RAG + G+++DQFAPRLSFFW IGMN+FMEVAK
Sbjct: 229 SGYHMQEAGATADLELAYTLADGVEYARAGVAAGMSIDQFAPRLSFFWAIGMNYFMEVAK 288

Query: 301 LRAARMLWAKLV-HQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGH 359
           +RAAR+LWA+L+  +F PK+ +S+SLRTHSQTSGWSL AQDV+NNV RTC+EAMAA  G 
Sbjct: 289 MRAARLLWARLMKREFDPKDDRSLSLRTHSQTSGWSLAAQDVFNNVARTCVEAMAAVNGQ 348

Query: 360 TQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARK 419
           TQSLHTNSLDEA+ALPTDFSARI+RNTQLFLQ ESGTTRV DPW GS YVE LT++LA+K
Sbjct: 349 TQSLHTNSLDEALALPTDFSARISRNTQLFLQMESGTTRVADPWGGSYYVERLTYELAQK 408

Query: 420 AWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLD 479
           A  HI+EVE +GGMAKAIE+G+PK+RIEEAAARTQARIDSG+Q ++GVN+Y+ E    + 
Sbjct: 409 ALAHIEEVEALGGMAKAIEQGLPKLRIEEAAARTQARIDSGKQSVVGVNRYKPEVADDIP 468

Query: 480 VLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAG 539
           VLKVDN  V A+Q  KL +L+AERDP   +AAL  +       D    D NLL L +DA 
Sbjct: 469 VLKVDNGAVRAQQLEKLARLKAERDPAATEAALTAL------EDGARGDGNLLALAVDAA 522

Query: 540 RAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPR 599
           RA ATVGE+S ALEKVFGR+ A+I++I GVY KE  N P    A+ +VE FEQA+GRRPR
Sbjct: 523 RAKATVGEISYALEKVFGRHRAEIKSIQGVYMKEAGNDPTAARAKAMVEAFEQADGRRPR 582

Query: 600 ILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAG 659
           IL+AKMGQDGHDRGQKVIATA+ADLGFDVD+GPLFQTP E ARQAVE DVHVVG SSLA 
Sbjct: 583 ILIAKMGQDGHDRGQKVIATAFADLGFDVDIGPLFQTPAEAARQAVENDVHVVGASSLAA 642

Query: 660 GHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLV 719
           GHLTL P L+ EL K GR DIL+ VGGVIP QDF  LR  GA  I+ PGTVI E+AI L+
Sbjct: 643 GHLTLAPELKAELAKQGRDDILMVVGGVIPPQDFQALRDAGAAAIFPPGTVIAEAAIELL 702

Query: 720 KKLRASL 726
           ++L   L
Sbjct: 703 EQLNRQL 709


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: 1413
Number of extensions: 49
Number of successful extensions: 4
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: 714
Length adjustment: 40
Effective length of query: 688
Effective length of database: 674
Effective search space:   463712
Effective search space used:   463712
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:

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