GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cadA in Herbaspirillum seropedicae SmR1

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate HSERO_RS17280 HSERO_RS17280 lysine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS17280 HSERO_RS17280 lysine
           decarboxylase
          Length = 750

 Score =  729 bits (1882), Expect = 0.0
 Identities = 364/755 (48%), Positives = 498/755 (65%), Gaps = 17/755 (2%)

Query: 6   KFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVA 65
           +FP++I+  D +++  +G  +R +A  +E +G  +L   S  +    A      +  +++
Sbjct: 4   RFPIVIIDEDFRSENTSGLGIRALADAIEAEGMEVLGVTSYGDLAQFAQQQSRASAFILS 63

Query: 66  AE----GAG---ENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQL 118
            +    GAG   E    L+ +   +   R +   +PI+  GE  T  + P + + +LH  
Sbjct: 64  IDDEEMGAGSDEETDHALKALRAFVSEIRHKNADIPIYLYGETRTSRHIPNDVLRELH-- 121

Query: 119 RGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYR 178
            G +++FEDT  F+AR + R A++YL GL PPFFRALV++    +YSWH PGH GGVA+ 
Sbjct: 122 -GFIHMFEDTPEFVARHIIREAKSYLDGLAPPFFRALVDYAQDGSYSWHCPGHSGGVAFL 180

Query: 179 KSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVING 238
           KSPVGQ FHQFFGE  LR+D+  +V ELG LLDHTGP+A +E  AAR F ADH +FV NG
Sbjct: 181 KSPVGQMFHQFFGERMLRADVCNAVEELGQLLDHTGPVANSERNAARIFNADHCYFVTNG 240

Query: 239 TSTANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSE 298
           TST+NK+VWHS V   D+V+VDRNCHKSILHSIIMTGAIP++L P RN LGIIGPIPL E
Sbjct: 241 TSTSNKMVWHSTVAPGDIVVVDRNCHKSILHSIIMTGAIPVFLMPTRNHLGIIGPIPLEE 300

Query: 299 FSKQSIAAKIAASPLAR-GREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEA 357
           F+ +SI  KI A+P AR  +  K ++  +T STYDG+ YN E +K  L   +E LHFDEA
Sbjct: 301 FTLESIQKKIEANPFAREAKNKKPRILTITQSTYDGVVYNVETLKDMLDGEIETLHFDEA 360

Query: 358 WYAYAAFHEFYDGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDV 416
           W  +A FH+FY   + +G  R   +  L+F+T STHK+LA  SQAS I V++  T KLD 
Sbjct: 361 WLPHATFHDFYKDMHAIGKDRPRAKKSLIFSTQSTHKLLAGLSQASQILVRESETVKLDE 420

Query: 417 ARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNL 476
             FNEAF+MH STSPQY IIAS DVA+AMME P G +L++E+  EAL FRRA+  + Q  
Sbjct: 421 DAFNEAFLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESILEALDFRRAMKKIDQEF 480

Query: 477 DRNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLS 536
             ++WWF VW P            DWV++   DWHGFG++A  + +LDPIK T+  PGL+
Sbjct: 481 G-DEWWFQVWGPNSFAADGIGEREDWVIKAEDDWHGFGNLAPGFNMLDPIKATIVNPGLA 539

Query: 537 AGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRC 596
             G+  E GIPA+IV+++L E G++VEK GLYSF ++F++GITKG+W+TLVT L +FK  
Sbjct: 540 LNGQFGETGIPASIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNTLVTALQQFKDD 599

Query: 597 YDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEVAMR 656
           YD N P+  +LP  AQ    RY  +GLRDL   +H +YR    A+    MY    + AM+
Sbjct: 600 YDKNQPIWRILPEFAQR-NPRYERLGLRDLCQQIHETYRAYDVARLTTEMYLSDMQPAMK 658

Query: 657 PSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFA 716
           PS+A+ K+   E+E VP+  LEGR+ +++L PYPPGIPL++PGE F    ++I+DYL+FA
Sbjct: 659 PSDAFSKMAHREIERVPLDELEGRVTSILLTPYPPGIPLLIPGEIF---NKTIVDYLKFA 715

Query: 717 RTFERAFPGFDSDVHGLQHQDGPSGRCYTVECIKE 751
           R F   FPGF++DVHGL  ++    R Y V+C+K+
Sbjct: 716 RDFNEKFPGFETDVHGLVKREVNGRRDYFVDCVKQ 750


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: 1437
Number of extensions: 41
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: 750
Length adjustment: 40
Effective length of query: 711
Effective length of database: 710
Effective search space:   504810
Effective search space used:   504810
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.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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