Aligments for a candidate for cadA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for cadA in Sinorhizobium meliloti 1021

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate SMa0682 SMa0682 decarboxylase (lysine, ornithine, arginine)

Query= SwissProt::Q9I2S7
         (751 letters)



>lcl|FitnessBrowser__Smeli:SMa0682 SMa0682 decarboxylase (lysine,
           ornithine, arginine)
          Length = 756

 Score =  863 bits (2231), Expect = 0.0
 Identities = 429/748 (57%), Positives = 544/748 (72%), Gaps = 8/748 (1%)

Query: 7   FPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAA 66
           FP+ ++  D +  + AG  +R +A  +E++G+ +++  +  + R + +  +  +C L++ 
Sbjct: 7   FPIAVIDEDYEGKSAAGRGMRSLAEAIEKEGYRVVAGLTYEDARRLVNVFNTESCWLISV 66

Query: 67  EGAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLFE 126
           +G   +    + + EL+   R R   LPIF  G+  T E  PA     L      + LFE
Sbjct: 67  DGTESSTTRWEILAELLAAKRSRNNLLPIFLFGDDTTAEMVPAPV---LRHANAFMRLFE 123

Query: 127 DTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAF 186
           D+  F+AR + RAA+NYL  L PP F+AL+E+T    YSWHTPGHGGGVA+RKSPVGQ F
Sbjct: 124 DSPEFMARAIVRAAQNYLERLPPPMFKALMEYTLHGAYSWHTPGHGGGVAFRKSPVGQLF 183

Query: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIV 246
           + FFGENTLRSD+SVSV  +GSLLDH GP+ E E  AAR FGAD T FV+ GTSTANKIV
Sbjct: 184 YTFFGENTLRSDISVSVGSVGSLLDHVGPIGEGERNAARIFGADETLFVVGGTSTANKIV 243

Query: 247 WHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAA 306
           W  MV R DLVL DRNCHKSILHS+IMTGA P+YLTP RN LGIIGPI   +F+ ++IA 
Sbjct: 244 WQGMVTRNDLVLCDRNCHKSILHSLIMTGATPIYLTPSRNGLGIIGPIAKEQFTPEAIAH 303

Query: 307 KIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHE 366
           KI ASP A     KV+L VVTNSTYDGLCYN + IK  LGD+VEVLHFDEAW+AYA FHE
Sbjct: 304 KIVASPFASETNGKVRLMVVTNSTYDGLCYNVDGIKSALGDAVEVLHFDEAWFAYANFHE 363

Query: 367 FYDGRYGMGT---SRSEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFNEAF 423
           FYDG + + +   +RS+E  + FAT STHK+LAAFSQASM+HVQ    ++LD+ RFNEAF
Sbjct: 364 FYDGYHAISSTKPARSQEA-ITFATQSTHKLLAAFSQASMLHVQHAVAKQLDITRFNEAF 422

Query: 424 MMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRNDWWF 483
           MMH STSPQYGIIAS DVA+AMME PAGR+L+QET DEA+SFRRA+  VR  + ++ WWF
Sbjct: 423 MMHTSTSPQYGIIASCDVAAAMMEQPAGRALVQETIDEAMSFRRAVNAVRTQM-QDSWWF 481

Query: 484 GVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGKLSE 543
            VW+P   +      T DW+L+P   WHGF D+AE++V++DPIKVT+ +PGL+AGG + E
Sbjct: 482 EVWEPPIADRAPSDATSDWLLKPGDAWHGFEDLAENHVMVDPIKVTILSPGLNAGGAMLE 541

Query: 544 QGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDANLPL 603
            GIPAA+V++FL  R + +EKTGLYSFLVLFSMGIT+GKWSTL+TELL FK  YDAN PL
Sbjct: 542 HGIPAAVVTKFLSSRRIEIEKTGLYSFLVLFSMGITRGKWSTLITELLNFKDLYDANAPL 601

Query: 604 LDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEAYDK 663
              LP++A A    Y  +GLRDL + +H  YR +    A + MYTVLPE+A+RP++AY++
Sbjct: 602 SRALPALAAAHPDVYRAMGLRDLCEKIHDVYRSDGVPNAQREMYTVLPEMALRPADAYNR 661

Query: 664 LVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFERAF 723
           LV+G VE+V I  L GR  AVM+VPYPPGIPLIMPGER T ATRSI DYL +AR+F+R F
Sbjct: 662 LVKGCVESVDIDELIGRTLAVMIVPYPPGIPLIMPGERITAATRSIQDYLVYARSFDRKF 721

Query: 724 PGFDSDVHGLQHQDGPSGRCYTVECIKE 751
           PGF++D+HGL+    PSGR Y V+CI E
Sbjct: 722 PGFETDIHGLRFVANPSGRRYLVDCIVE 749


Lambda     K      H
   0.320    0.136    0.407 

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: 1454
Number of extensions: 47
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: 751
Length of database: 756
Length adjustment: 40
Effective length of query: 711
Effective length of database: 716
Effective search space:   509076
Effective search space used:   509076
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 (21.8 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