Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate RR42_RS15940 RR42_RS15940 lysine decarboxylase
Query= BRENDA::E8X9U7 (756 letters) >FitnessBrowser__Cup4G11:RR42_RS15940 Length = 754 Score = 541 bits (1393), Expect = e-158 Identities = 292/769 (37%), Positives = 446/769 (57%), Gaps = 38/769 (4%) Query: 4 VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDD--GYAILSANEA-----ID 56 V+I++ +F ++ G+ + LA A+ Q+ + V+ TS+ D +A S+ + ID Sbjct: 7 VIIIDEDFRSENI-SGSGIRALAQAIEQEGMEVMGLTSYGDLTSFAQQSSRASSFIVSID 65 Query: 57 CLMFSYQMEQPDEHL--SVRQLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFA 114 F + ++P+ +R + ++ R ++P+FL G+ + + + D+L + F Sbjct: 66 DDEFVSEDDRPEAAAIEKLRAFVNEVRRRNTDLPIFLYGET-RTSRHIPNDILRELHGFI 124 Query: 115 WILEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPA 174 + EDT +F+A + Y L PP F AL+ Y+ YSW PGH GGV F K+P Sbjct: 125 HMFEDTPEFVARHIIREARVYLDSLAPPFFKALIAYAQDSSYSWHCPGHSGGVAFLKSPV 184 Query: 175 GRFYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGS 234 G+ +H ++GEN+ R+D+ LG LLDHTG SE+NAAR+F +D + V GTS S Sbjct: 185 GQVFHQFFGENMLRADVCNAVDELGQLLDHTGPVAASERNAARIFNSDHMYFVTNGTSTS 244 Query: 235 NRTIMQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPE 294 N+ + A + D+VV+DRNCHKSI +++TGA PV+++P+RN YGIIGPI E PE Sbjct: 245 NKMVWHANVAPGDIVVVDRNCHKSILHAIMMTGAIPVFLMPTRNHYGIIGPIPKSEFDPE 304 Query: 295 TLQKKISASPLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGY 354 T+++KI+A P QKP +T TYDGV YNA++ +++LA D +HFDEAW + Sbjct: 305 TIRRKIAAHPFASQAKNQKPRILTITQGTYDGVLYNAEQIKEMLATEIDTLHFDEAWLPH 364 Query: 355 ARFNPIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREG-RGAVNFSRFN 413 A F+ Y + +A+ + VFAT STHKLL LSQAS I V++ ++ RFN Sbjct: 365 AAFHDFYHNMHAIGRDRPRSKDALVFATQSTHKLLAGLSQASQILVQDSDTRKLDRYRFN 424 Query: 414 QAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFT--D 471 +AY+MH +TSP Y+I AS DVA +MM+ G +L +E I EA+DFR+AM ++ ++ + Sbjct: 425 EAYLMHTSTSPQYSIIASCDVAAAMMEAPGGTALVEESIQEAMDFRRAMRKVEGDYDAGN 484 Query: 472 EGDWFFKPWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSM 531 GDW+FK W + + + G D+ W+++ E WHGF DL D +++ Sbjct: 485 NGDWWFKVWGPEALAEDDIG---------------DREEWMLKANERWHGFGDLADGFNL 529 Query: 532 LDPIKVSILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGK 591 LDPIK +I+ PG+ DGE G+PAA+VT +L HGI+ +T + +F++G+T+G+ Sbjct: 530 LDPIKATIITPGLDVDGEFSDRGIPAAIVTKYLAEHGIIIEKTGLYSFFIMFTIGITKGR 589 Query: 592 WGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGAR 651 W +L+ L FK YD N PL +V+PE V +P Y +G+ DL D + + + N+ Sbjct: 590 WNSLVTELQQFKDDYDQNQPLWRVLPEFVGKHPQ-YEKLGLRDLCDAIHSVYKANDVARV 648 Query: 652 LNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENF 711 Y + + P DA+ + + IE VA++ L GR+ A + PYPPGIP+L+ GE F Sbjct: 649 TTEMYLSDMEPAMKPSDAWAMMAHREIERVAVDELEGRVTAILLTPYPPGIPLLIPGERF 708 Query: 712 GDENSPQVGYLRSLQSWDHHFPGFEHETEG--TEIIDG---VYHVMCVK 755 N V YL+ + ++ FPGFE + G E ++G Y V CVK Sbjct: 709 ---NRIIVQYLKFAREFNKLFPGFETDIHGLVEEEVEGGGKAYFVDCVK 754 Lambda K H 0.319 0.135 0.415 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: 1427 Number of extensions: 71 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: 756 Length of database: 754 Length adjustment: 40 Effective length of query: 716 Effective length of database: 714 Effective search space: 511224 Effective search space used: 511224 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.
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:
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