Aligments for a candidate for odc in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources