Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate 199509 SO0314 ornithine decarboxylase, inducible (NCBI ptt file)
Query= SwissProt::Q9I2S7 (751 letters) >FitnessBrowser__MR1:199509 Length = 720 Score = 365 bits (938), Expect = e-105 Identities = 229/644 (35%), Positives = 325/644 (50%), Gaps = 30/644 (4%) Query: 118 LRGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAY 177 + G+ L F +QV A + Y LLPPFF L ++ N ++ PGH GG + Sbjct: 78 ITGVFELCGSNTDFYGKQVETAIKKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFF 137 Query: 178 RKSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVIN 237 RK PVG+ F FFGE RSD+ + +LG LL H G +A+ AA+ F AD T+FV+N Sbjct: 138 RKHPVGRQFFDFFGETIFRSDMCNADVKLGDLLIHEGAPLDAQKYAAKVFNADKTYFVLN 197 Query: 238 GTSTANKIVWHSMVGREDLVLVDRNCHKSILH-SIIMTGAIPLYLTPERNELGIIGPIPL 296 GTS++NK+ ++++ + DLVL DRN HKS H ++I GA P+YL RN G IG I Sbjct: 198 GTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGALIQAGATPIYLETARNPFGFIGGIDA 257 Query: 297 SEFSKQSIAAKIAASPLARGREPK-VKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFD 355 F + + +I R E + +LA++ TYDG YNA + +G + + FD Sbjct: 258 HCFKEAYLREQIREVAPERADEKRPFRLAIIQLGTYDGTIYNARQVVDRIGHLCDYILFD 317 Query: 356 EAWYAYAAFHEFYDGRYGMGTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQD----GGT 411 AW Y F + + + E P + T S HK A FSQ S IH +D G Sbjct: 318 SAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQA 377 Query: 412 RKLDVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALAN 471 R + RFN AFMMH STS Y + A+LDV + M EG +GR L +E + R+ L Sbjct: 378 RYCNHKRFNNAFMMHASTSHFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLK 437 Query: 472 --------VRQNLDRNDWWFGVWQPEQVEGTDQVG--THDWVLEPSADWHGFGDIAEDYV 521 + +D W Q T+Q+ + EP WH F + Sbjct: 438 KCKYIKPFIPSMIDGRQW--------QDYPTEQMADDLRFFEFEPGQKWHSFEGYEKGQY 489 Query: 522 LLDPIKVTLTTPGLSA-GGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITK 580 +DP K LTTPG+ A GK +E GIPA I++ FL E ++ EK L S L L + Sbjct: 490 FVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDM 549 Query: 581 GKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATA 640 K LV+++ F++ D + PL +VLP+V A RY +R L MH Y + Sbjct: 550 AKMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVK 609 Query: 641 KAMKRMY--TVLPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMP 698 + K M+ P M P EA + +RG VE VP++++EGRIAA +PYPPG+ ++P Sbjct: 610 QLQKEMFRHAHFPTKVMDPQEANLEFIRGNVELVPLSQIEGRIAAEGALPYPPGVLCMVP 669 Query: 699 GERFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSGR 742 GE + A + LE PGF ++ G+ + P G+ Sbjct: 670 GEIWGGAVQRYFLALEEGINL---LPGFSPELQGVYLESTPDGK 710 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: 1141 Number of extensions: 66 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: 720 Length adjustment: 40 Effective length of query: 711 Effective length of database: 680 Effective search space: 483480 Effective search space used: 483480 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