GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cadA in Chromobacterium vaccinii MWU205

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate WP_046156677.1 VL52_RS08800 arginine/lysine/ornithine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>NCBI__GCF_000971335.1:WP_046156677.1
          Length = 752

 Score =  717 bits (1852), Expect = 0.0
 Identities = 367/758 (48%), Positives = 491/758 (64%), Gaps = 23/758 (3%)

Query: 7   FPVLIVHRDIKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAA 66
           FP++I+  D +++  +G  +R +A  +E +G S++   S  +    A      A  +++ 
Sbjct: 5   FPIVIIDEDFRSENTSGSGIRELAAAMEAEGMSVIGYTSYGDLTSFAQQQSRAAGFILSI 64

Query: 67  EG-----AGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGI 121
           +          Q  L ++   +   R R P +P++  GE  T  + P + + +LH   G 
Sbjct: 65  DDEEFQTVDSAQESLGNLYGFVAEIRRRNPDIPVYLYGETRTARHIPNDILRELH---GF 121

Query: 122 LYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSP 181
           +++ EDT  F+AR + R A++YL  L PPFFRALV++    +YSWH PGH GGVA+ KSP
Sbjct: 122 IHMHEDTPEFVARHIIREAKSYLDNLAPPFFRALVDYAYDGSYSWHCPGHSGGVAFLKSP 181

Query: 182 VGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTST 241
           VGQ FHQFFGEN LR+D+  +V ELG LLDHTGP+A +E  AAR F ADH FFV NGTST
Sbjct: 182 VGQMFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNADHLFFVTNGTST 241

Query: 242 ANKIVWHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSK 301
           +NKIVWHS V   D+VLVDRNCHKS LH+IIMTGAIP++L P RN  GIIGPIP SEF  
Sbjct: 242 SNKIVWHSCVAAGDIVLVDRNCHKSNLHAIIMTGAIPVFLMPTRNHYGIIGPIPKSEFQP 301

Query: 302 QSIAAKIAASPLAR-------GREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHF 354
            +I  KI A+P AR        R+P++    +T STYDG+ YN E IK  L   V+ LHF
Sbjct: 302 DTIKKKILANPFAREMLEQRPNRKPRI--LTLTQSTYDGILYNVEEIKGLLDGEVDTLHF 359

Query: 355 DEAWYAYAAFHEFYDGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQDGGTRK 413
           DEAW  +A FH+FY   + +G  R   E  LVF+T STHK+LA  SQAS I VQD   R+
Sbjct: 360 DEAWLPHACFHDFYRDFHAIGEGRPRCEDSLVFSTQSTHKLLAGISQASQILVQDPQNRQ 419

Query: 414 LDVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVR 473
           LD A FNEA++MH STSPQY IIAS DVA+AMME P G+SL++E+  EA+ FRRA+  V 
Sbjct: 420 LDTAWFNEAYLMHTSTSPQYSIIASCDVAAAMMEQPGGQSLVEESLVEAMEFRRAMRKVD 479

Query: 474 QNLDRNDWWFGVWQPEQVEGTDQVGTHDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTP 533
           +   R DWWF VW P+ +         DW L P   WHGF  I + + +LDPIK T+ TP
Sbjct: 480 EEYGR-DWWFSVWGPDDLSDDGICDQTDWTLRPDERWHGFAGIEDGFNMLDPIKATVLTP 538

Query: 534 GLSAGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEF 593
           GL   G   E GIPAAIV+++L E G+VVEKTGLYSF ++F++GITKG+W+TL++ L +F
Sbjct: 539 GLDVDGSFEEMGIPAAIVTKYLTEHGVVVEKTGLYSFFIMFTIGITKGRWNTLISLLQQF 598

Query: 594 KRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYTVLPEV 653
           K  +D N PL  V+P    A   +Y+ VGL+DL   +H  Y  +  A+    +Y    E 
Sbjct: 599 KDDFDKNQPLWRVMPEFV-AKYPQYDRVGLQDLCQRIHGLYTKHDVARLTTDIYLSDMEP 657

Query: 654 AMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYL 713
           AMRP++A+ K+   E+E VP+ +LEGR+ AV+L PYPPGIPL++PGERF    ++I+DYL
Sbjct: 658 AMRPADAFAKMAHREIERVPVDQLEGRVTAVLLTPYPPGIPLLIPGERF---NKTIVDYL 714

Query: 714 EFARTFERAFPGFDSDVHGLQHQDGPSGRCYTVECIKE 751
            FA+ F R  PGF++DVHGL   +    + Y V+C+K+
Sbjct: 715 RFAQAFNRELPGFETDVHGLVAVEVQDRKVYCVDCVKQ 752


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: 1397
Number of extensions: 46
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: 752
Length adjustment: 40
Effective length of query: 711
Effective length of database: 712
Effective search space:   506232
Effective search space used:   506232
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 24 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