GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcmA in Azospirillum brasilense Sp245

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS24250 AZOBR_RS24250 methylmalonyl-CoA mutase

Query= BRENDA::Q84FZ1
         (721 letters)



>FitnessBrowser__azobra:AZOBR_RS24250
          Length = 732

 Score = 1080 bits (2793), Expect = 0.0
 Identities = 546/729 (74%), Positives = 622/729 (85%), Gaps = 14/729 (1%)

Query: 5   IPDFASVAYAADGFKAPPP-------------PAGEPWMTPEGIPVKGFYGPEDREGCEG 51
           +PDF+++   A    A P              PA   W TPE + VK  Y   D +G + 
Sbjct: 4   LPDFSTLPLDAAVSNASPAEWSRRFAAETGTDPATALWRTPEMLDVKPLYTAADLDGLDH 63

Query: 52  IDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLA 111
           + + PG+ P+LRGPYP MYV +PWT+RQYAGFSTA++SNAFYRRNLAAGQKGLSVAFDLA
Sbjct: 64  LAAMPGMAPFLRGPYPTMYVDKPWTVRQYAGFSTAQESNAFYRRNLAAGQKGLSVAFDLA 123

Query: 112 THRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIV 171
           THRGYDSDHPRV+GDVGMAGVAIDSI DM+TLF GIPLD+M+VSMTMNGAVLP +A YIV
Sbjct: 124 THRGYDSDHPRVTGDVGMAGVAIDSILDMKTLFDGIPLDQMSVSMTMNGAVLPVLAGYIV 183

Query: 172 AAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISI 231
           AAEEQGV  +KL+GTIQNDILKEFMVRNTYIYPPK SMRIISDIF +TS++MPKFNSISI
Sbjct: 184 AAEEQGVSADKLSGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAFTSQHMPKFNSISI 243

Query: 232 SGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAK 291
           SGYH+QEAGAT DLELAYTLADGVEY +AGLAAGLTIDQFAPRLSFFWAIGMNFFME+AK
Sbjct: 244 SGYHLQEAGATADLELAYTLADGVEYARAGLAAGLTIDQFAPRLSFFWAIGMNFFMEVAK 303

Query: 292 MRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGT 351
           MRA R++WAKL+KEF PKSDKSL LRTHSQTSGWSLTAQDVFNNVTRTCIEAMA+TQG T
Sbjct: 304 MRAGRMLWAKLIKEFAPKSDKSLSLRTHSQTSGWSLTAQDVFNNVTRTCIEAMASTQGHT 363

Query: 352 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARA 411
           QSLHTNALDEALALPTDFSARIARNTQLFLQQESGT R+IDPWGGSYYVERLTR++AARA
Sbjct: 364 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGTCRVIDPWGGSYYVERLTRELAARA 423

Query: 412 WEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDL 471
           W HIREVE  GGMAKAIE GIPK+R+EEAAAR QARIDSGRQT+VG+NKY+ + E  I++
Sbjct: 424 WGHIREVEETGGMAKAIETGIPKMRVEEAAARTQARIDSGRQTVVGVNKYRLEQEEAIEV 483

Query: 472 LRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTK-AADGEGNLLELAVNAARAKATV 530
           L+VDN+ VRA+QI +L+RLRAER+       L ALT  AA G+GNLL L+V+A RA+ATV
Sbjct: 484 LKVDNSAVRAQQIAQLERLRAERDPIRCRQTLEALTNAAAAGDGNLLALSVDAIRARATV 543

Query: 531 GEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAK 590
           GEIS+ALEK +GRH+A+IR+I+G+Y  EVG  S  + +VR LV  F E DGRRPRI+VAK
Sbjct: 544 GEISDALEKVYGRHKAEIRTITGIYAGEVGRQSDAIARVRALVAEFAERDGRRPRIMVAK 603

Query: 591 MGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTL 650
           MGQDGHDRGQKVIA+AFADLGFDVD+GPLF TP+EAARQAVEND HIVGVSSLAAGHLTL
Sbjct: 604 MGQDGHDRGQKVIATAFADLGFDVDVGPLFQTPEEAARQAVENDCHIVGVSSLAAGHLTL 663

Query: 651 VPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNT 710
           VP+LKA L++ G  D++IVVGGV+PP DYDALYAAGA+AIFPPGTVI+EAAV+LL  LN 
Sbjct: 664 VPQLKAELERHGAGDILIVVGGVVPPQDYDALYAAGATAIFPPGTVISEAAVDLLRILNE 723

Query: 711 RLGYGERQA 719
           R GY  + A
Sbjct: 724 RHGYAPKAA 732


Lambda     K      H
   0.318    0.134    0.391 

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: 1398
Number of extensions: 37
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: 721
Length of database: 732
Length adjustment: 40
Effective length of query: 681
Effective length of database: 692
Effective search space:   471252
Effective search space used:   471252
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