GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cadA in Burkholderia phytofirmans PsJN

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate BPHYT_RS04980 BPHYT_RS04980 lysine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS04980 BPHYT_RS04980 lysine
           decarboxylase
          Length = 761

 Score =  738 bits (1906), Expect = 0.0
 Identities = 373/765 (48%), Positives = 500/765 (65%), Gaps = 28/765 (3%)

Query: 6   KFPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVA 65
           +FPV+I+  D +++ ++G  +R +A  +E++G  +L   S  +    A      +C +++
Sbjct: 4   RFPVVIIDEDFRSENISGSGIRALAEAIEKEGAEVLGLTSYGDLTSFAQQSSRASCFILS 63

Query: 66  AEG------------AGENQRLLQDVVEL---IRVARVRAPQLPIFALGEQVTIENAPAE 110
            +              GE   L   +V L   +   R R   +PIF  GE  T  + P +
Sbjct: 64  IDDDELLPYVDNVVVEGETPELAAAIVALRAFVTEVRRRNADIPIFLYGETRTSRHLPND 123

Query: 111 SMADLHQLRGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPG 170
            + +LH   G +++FEDT  F+AR + R  + YL  L PPFF+ LV++  + +YSWH PG
Sbjct: 124 ILRELH---GFIHMFEDTPEFVARHIIRETKVYLDSLAPPFFKELVQYADEGSYSWHCPG 180

Query: 171 HGGGVAYRKSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGAD 230
           H GGVA+ KSP+GQ FHQFFGEN LR+D+  +V ELG LLDHTGP+A +E  AAR F AD
Sbjct: 181 HSGGVAFLKSPLGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFSAD 240

Query: 231 HTFFVINGTSTANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGI 290
           H FFV NGTST+NKIVWH  V   D+VLVDRNCHKSILH+I MTGAIP++LTP RN  GI
Sbjct: 241 HVFFVTNGTSTSNKIVWHGTVAPGDIVLVDRNCHKSILHAITMTGAIPVFLTPTRNNFGI 300

Query: 291 IGPIPLSEFSKQSIAAKIAASPLAR---GREPKVK--LAVVTNSTYDGLCYNAELIKQTL 345
           IGPIP SEF  ++I  KI A+P AR    + P +K  +  +T STYDG+ YN E+IK+ L
Sbjct: 301 IGPIPRSEFEPENIKKKILANPFAREALAKNPNLKPRILTITQSTYDGVIYNVEMIKEML 360

Query: 346 GDSVEVLHFDEAWYAYAAFHEFYDGRYGMGTSRSEEGPLVFATHSTHKMLAAFSQASMIH 405
           GD ++ LHFDEAW  +A FHEFY   + +G  R   G +VFATHSTHK+LA  SQAS I 
Sbjct: 361 GDWLDTLHFDEAWLPHAEFHEFYQDMHAIGAGRPRIGAMVFATHSTHKLLAGISQASQIV 420

Query: 406 VQDGGTRKLDVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSF 465
           VQD    + D  RFNEA++MH STSPQY IIAS DVA+AMME P G +L++E+  EAL F
Sbjct: 421 VQDSKNSRFDKHRFNEAYLMHTSTSPQYAIIASCDVAAAMMEAPGGPALVEESIAEALDF 480

Query: 466 RRALANVRQNLDRNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDP 525
           RRA+  V      +DW+F VW P+Q          DW+L P+ +WHGFG +A+++ +LDP
Sbjct: 481 RRAMIKVDAEYG-DDWFFKVWGPDQFAEEGIGSREDWMLRPNDEWHGFGPLADNFNMLDP 539

Query: 526 IKVTLTTPGLSAGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWST 585
           IK T+ TPGL  GG   E GIPAAIV+++L E G++VEKTGLYSF ++F++GITKG+W++
Sbjct: 540 IKATIVTPGLDMGGGFGETGIPAAIVTKYLAEHGIIVEKTGLYSFFIMFTIGITKGRWNS 599

Query: 586 LVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKR 645
           +VTEL +FK  YD N PL  VLP    +    Y  VGLRDL   +H+ YR N  A+    
Sbjct: 600 MVTELQQFKDDYDNNQPLWRVLPEFV-SHHPMYERVGLRDLCQQIHSVYRANDIARLTTE 658

Query: 646 MYTVLPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEA 705
           MY    E AM+PS+A+ KL   E++ VPI  LEGR+ +++L PYPPGIPL++PGERF   
Sbjct: 659 MYLSSMEPAMKPSDAFAKLAHREIDRVPIDELEGRVTSILLTPYPPGIPLLIPGERF--- 715

Query: 706 TRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSGRCYTVECIK 750
            ++I++YL FAR F   FPGF +D+HGL  +       Y V+C++
Sbjct: 716 NKTIVNYLRFAREFNERFPGFHTDIHGLVGETINGRIEYFVDCVR 760


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: 1478
Number of extensions: 60
Number of successful extensions: 6
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: 761
Length adjustment: 40
Effective length of query: 711
Effective length of database: 721
Effective search space:   512631
Effective search space used:   512631
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 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