GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Sinorhizobium meliloti 1021

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate SMa0680 SMa0680 amino acid (ornithine, lysine, arginine) decarboxylase

Query= BRENDA::A4Q8H0
         (720 letters)



>FitnessBrowser__Smeli:SMa0680
          Length = 782

 Score =  704 bits (1818), Expect = 0.0
 Identities = 376/743 (50%), Positives = 482/743 (64%), Gaps = 41/743 (5%)

Query: 16  FETE-REIVDVHQSDFNDVAAIVLSVE----DVAKGMVTHLEEIGLNIPLFVAVCCEEEL 70
           FE E R   +   S+   V A + +VE    + A+  V  + +IG   PL+         
Sbjct: 39  FEVELRGSYNADVSEDASVGAYIGTVEGGRLEDARKFVRAVRDIGFRTPLWALADSHGIA 98

Query: 71  DNAVLPALHGV--FELCGKNTQ-FYGKQLEAAAVKYEKDLLPPFFNTLTQYVEMGNATFA 127
           D A +     V  F   G+ T  FY KQ+ ++ V Y K LLPPFF  L  Y    N  F 
Sbjct: 99  DIAAIKMAGEVDGFVYLGQQTPAFYAKQIISSLVNYGKTLLPPFFGGLMAYDGEANIAFD 158

Query: 128 CPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCNADVKLGDLLIHEGLPCAAQQHAAKVF 187
           CPGHQGG+F+RK PAG+ FF+++GE++FR+D+CNADV LGDLLIHEG    AQ++AA++F
Sbjct: 159 CPGHQGGQFYRKSPAGQLFFNYFGESIFRADLCNADVDLGDLLIHEGPAAEAQKNAARIF 218

Query: 188 NADKTYFVLNGTSASNKVATNALLTRGDLVLFDRNNHKSNHHGALIQAGATPVYLETARN 247
            AD+TYF+LNGTS SNKV TNA+L  GDLVLFDRNNHKS H GAL+QAGA PVYL T+RN
Sbjct: 219 GADRTYFILNGTSTSNKVVTNAVLRAGDLVLFDRNNHKSLHQGALVQAGAIPVYLPTSRN 278

Query: 248 PFGFIGGIDAHCFDERYLRQQIRE----VAPERANEARPFRLAIIQLGTYDGTIYNARQV 303
            FG IG +D   +DE  LR+QI          RA+  RPFRLA IQL TYDGTIYN R+V
Sbjct: 279 SFGMIGAVDWDAWDEASLRRQIERHPLVEDKARASAERPFRLACIQLATYDGTIYNVRKV 338

Query: 304 VDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLE-LNENDPGIIVTQSVHKQQAGFSQ 362
           +++IGHLCDY+L+D AW+GY  F P+ +D SP+ ++ L+   PG+  TQSVHKQ AGFSQ
Sbjct: 339 LEQIGHLCDYVLWDEAWIGYNAFHPLFEDHSPMRIDTLDAEMPGLFSTQSVHKQGAGFSQ 398

Query: 363 TSQIHKKDKHIKGQSRYCNHKRFNNAFMLHASTSPFYPLFAALDVNAKMHEGKSGQRLWK 422
            SQIHK+D+HI+ Q RY  HKRFN + ++H STSPFYPLFA+LDVNAK+HEGK+G+ LW 
Sbjct: 399 ASQIHKRDEHIRDQRRYVEHKRFNESLLMHVSTSPFYPLFASLDVNAKIHEGKAGEMLWD 458

Query: 423 ECVRVGIEARKMLLETCQ-------------LIKPFVPD--QIDGKP---------WQSY 458
            C+ +GIEARK L E  +                PFVPD   I G           W++ 
Sbjct: 459 RCIELGIEARKKLREFTRYYESSGAGPQEQWFFDPFVPDVVTISGSKHTEDVVESRWEAL 518

Query: 459 DTETMANDLRFFNFVPGEKWHAFEGYAESQYFVDPCKLLLTTPGIDTASGNYSDFGIPAT 518
            TE +  + + + F PG  WH + GY++    VDP KL L TPGID A+G Y DFGIPAT
Sbjct: 519 PTEVIKREQQCWRFRPGASWHGYSGYSDGYAMVDPNKLTLLTPGIDRATGEYRDFGIPAT 578

Query: 519 ILANYLRENGIVPEKCDLNSILFLLTPAEDIAKMQHLVALIARFEKHIEQDSLLSEVLPA 578
           ++ANYLRE  IVPEKCDLNSILFLLTPAED +K+  L+A + +F+   ++D+ L+EVLP 
Sbjct: 579 MVANYLREQRIVPEKCDLNSILFLLTPAEDESKLNTLIAKLVKFKNLWDRDAPLAEVLPT 638

Query: 579 VYKSNEQRYKNYTLRQLCQEMHDLYVSYDVKELQKEMFRKNYFPRIAMNPQDANTEFVRG 638
           V+ +N +RY  YTLRQ+C EMHD Y    VKELQ+  FR    P  AM P+ A    V  
Sbjct: 639 VFAANRERYAGYTLRQVCAEMHDFYRQAGVKELQRLCFRAESMPEPAMTPKAAYEALVAN 698

Query: 639 NIELVSLAKAEGRIAAEGALPYPPGVLCVVPGEIWGGAAQ---RYFLALEEGINLLPGFA 695
            ++ V+L +A GRI+A  AL YPPG+  +VPGE W   A+    YFLA +E  N  PGF 
Sbjct: 699 EVDYVALDEAFGRISATLALIYPPGIGVIVPGERWDERARPMHNYFLAFQESFNRFPGFN 758

Query: 696 PELQGVYIQQDEDGWNRAYGYVM 718
            E+QGV+ Q+  DG  + Y Y +
Sbjct: 759 YEVQGVF-QERVDGQIKFYTYAV 780


Lambda     K      H
   0.321    0.138    0.420 

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: 1554
Number of extensions: 92
Number of successful extensions: 5
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: 720
Length of database: 782
Length adjustment: 40
Effective length of query: 680
Effective length of database: 742
Effective search space:   504560
Effective search space used:   504560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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