Alignments for a candidate for cadA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Paraburkholderia bryophila 376MFSha3.1

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate H281DRAFT_00160 H281DRAFT_00160 ornithine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__Burk376:H281DRAFT_00160
          Length = 761

 Score =  734 bits (1895), Expect = 0.0
 Identities = 372/765 (48%), Positives = 497/765 (64%), 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  IDDDELLPYVENVVVEGETPELAAAIVALRAFVTEVRRRNADIPIFLYGETRTSRHLPND 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 IGPIPLSEFSKQSIAAKIAASP-----LARGREPKVKLAVVTNSTYDGLCYNAELIKQTL 345
           IGPIP SEF  ++I  KI A+P     LA+  + K ++  +T STYDG+ YN E+IK+ L
Sbjct: 301 IGPIPRSEFEPENIRRKIEANPFAREALAKNPDLKPRILTITQSTYDGVIYNVEMIKEML 360

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

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

Query: 466 RRALANVRQNLDRNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDP 525
           RRA+  V      +DW+F VW P+Q          DW+L P+  WHGFG +AE + +LDP
Sbjct: 481 RRAMTKVDTEYG-DDWFFKVWGPDQFADEGIGSREDWMLRPNDSWHGFGPLAEGFNMLDP 539

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

Query: 586 LVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKR 645
           +VTEL +FK  YD N PL  VLP    A    Y  VGLRDL   +H+ YR N  A+    
Sbjct: 600 MVTELQQFKDDYDNNQPLWRVLPDFV-ALHPTYERVGLRDLCQQIHSVYRANDIARLTTE 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 NKTIVNYLRFAREFNERFPGFHTDIHGLVGEMINGRIEYFVDCVR 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: 1468
Number of extensions: 57
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:

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