GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMa0682
          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.

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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