Alignments for a candidate for cadA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Dechlorosoma suillum PS

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate Dsui_1245 Dsui_1245 arginine/lysine/ornithine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__PS:Dsui_1245
          Length = 746

 Score =  719 bits (1856), Expect = 0.0
 Identities = 361/752 (48%), Positives = 497/752 (66%), Gaps = 18/752 (2%)

Query: 7   FPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAA 66
           FPV+I+  D +++  +G  +R +A  ++ +G  +L   S  +    A      +  +++ 
Sbjct: 5   FPVIIIDEDFRSENASGLGIRALAEAIQAEGLEVLGVTSYGDLTSFAQQQSRASTFILSI 64

Query: 67  E-----GAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGI 121
           +         + + +  +   +   R+R  ++PIF  GE  T  + P + + +LH   G 
Sbjct: 65  DDEEFSSPEASAKAIAGLRAFVSEIRLRNSEIPIFLHGETRTSRHIPNDVLRELH---GF 121

Query: 122 LYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSP 181
           ++++EDT  F+AR V R A+ YL  L PPFFRAL  + +  +YSWH PGH GGVA+ KSP
Sbjct: 122 IHMYEDTPEFIARNVVREAKAYLESLPPPFFRALTHYASDGSYSWHCPGHSGGVAFLKSP 181

Query: 182 VGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTST 241
           VGQ FHQFFGEN LR+D+  +V ELG LLDHTGP+A +E  AAR F  DH +FV NGTST
Sbjct: 182 VGQMFHQFFGENMLRADVCNAVEELGQLLDHTGPVAASERNAARIFNCDHLYFVTNGTST 241

Query: 242 ANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSK 301
           +NKIVWHS V   D+V+VDRNCHKSILH+I+MTGAIP++L P RN  GIIGPIP SEF+ 
Sbjct: 242 SNKIVWHSTVAPGDIVVVDRNCHKSILHAIMMTGAIPVFLMPTRNNFGIIGPIPKSEFAW 301

Query: 302 QSIAAKIAASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAY 361
           ++I  KIAA+P A  +  K ++  +T STYDG+ YN E IK+ L   ++ LHFDEAW  +
Sbjct: 302 ENIQKKIAANPFATDKNAKPRVLTITQSTYDGILYNVEAIKEELDGKIDTLHFDEAWLPH 361

Query: 362 AAFHEFYDGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFN 420
           AAFH+FY   + +G  R   +  +VF+T STHK+LA  SQAS I VQD     LD   FN
Sbjct: 362 AAFHDFYGDYHAIGADRPRCKESMVFSTQSTHKLLAGLSQASQILVQDAENSHLDRDVFN 421

Query: 421 EAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRND 480
           EA++MH STSPQY IIAS DVA+AMME P G +L++E+  EAL FRRA+  V +    + 
Sbjct: 422 EAYLMHTSTSPQYAIIASCDVAAAMMEEPGGTALVEESIAEALDFRRAMRKVDEEWG-SG 480

Query: 481 WWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSAGGK 540
           WWF VW P+ +          W+L+P   WHGFG++A+ + +LDPIK T+ TPGL   G+
Sbjct: 481 WWFKVWGPDDLSEEGIEERDAWMLKPGDRWHGFGNLADGFNMLDPIKATIITPGLDVDGE 540

Query: 541 LSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDAN 600
            +E+GIPAAIV+++L E G++VEK GLYSF ++F++GITKG+W+++VTEL +FK  YD N
Sbjct: 541 FAERGIPAAIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNSMVTELQQFKDDYDKN 600

Query: 601 LPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMRPSEA 660
            PL  VLP+   A   RY  VGLRDL   +HA YR N  A+    MY      AM+P++A
Sbjct: 601 QPLWKVLPAFV-AKHPRYERVGLRDLCREIHAVYRSNDVARLTTEMYLSDMVPAMKPADA 659

Query: 661 YDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFE 720
           + K+   E++ VPI  LEGR+ +V+L PYPPGIPL++PGERF    R+I+ YL+FAR F 
Sbjct: 660 FAKMAHREIDRVPIDELEGRVTSVLLTPYPPGIPLLIPGERF---NRTIMQYLQFARDFN 716

Query: 721 RAFPGFDSDVHGL--QHQDGPSGRCYTVECIK 750
             FPGF++D+HGL  + +DG  G  Y V+C++
Sbjct: 717 EKFPGFETDIHGLVKEERDGKVG--YYVDCVR 746


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: 1380
Number of extensions: 52
Number of successful extensions: 7
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: 746
Length adjustment: 40
Effective length of query: 711
Effective length of database: 706
Effective search space:   501966
Effective search space used:   501966
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
the source code
instructions for running GapMind on your computer

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