Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate 14824 b0693 ornithine decarboxylase isozyme, inducible (NCBI)
Query= SwissProt::Q9I2S7 (751 letters) >FitnessBrowser__Keio:14824 Length = 732 Score = 367 bits (941), Expect = e-105 Identities = 239/676 (35%), Positives = 345/676 (51%), Gaps = 36/676 (5%) Query: 93 LPIFALGEQVTIENAPAESMADLHQLRGILYLFEDTVPFLARQVARAARNYLAGLLPPFF 152 +P+F E E PAE L ++ G+ E F RQ+ AA +Y L PPFF Sbjct: 58 IPVFIATENQ--ERVPAEY---LPRISGVFENCESRREFYGRQLETAASHYETQLRPPFF 112 Query: 153 RALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDH 212 RALV++ Q N ++ PGH GG +R+ P G F ++FGE R+DL + +G LL H Sbjct: 113 RALVDYVNQGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIH 172 Query: 213 TGPLAEAEDRAARNFGADHTFFVINGTSTANKIVWHSMVGREDLVLVDRNCHKSILH-SI 271 G A+ AA+ F AD T+FV+NGTS++NK+V ++++ DLVL DRN HKS H ++ Sbjct: 173 EGAPCIAQQHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGAL 232 Query: 272 IMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAAKIAASPLARGREPK-VKLAVVTNST 330 + GA P+YL RN G IG I F + + IA R +E + +LAV+ T Sbjct: 233 LQAGATPVYLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGT 292 Query: 331 YDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHEFYDGRYGMGTSRSEEGPLVFATHS 390 YDG YNA + +G + + FD AW Y F + +E P + T S Sbjct: 293 YDGTIYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQS 352 Query: 391 THKMLAAFSQASMIHVQD----GGTRKLDVARFNEAFMMHISTSPQYGIIASLDVASAMM 446 HK A FSQ S IH +D G R + R N AFMMH STSP Y + A+L++ + M Sbjct: 353 VHKQQAGFSQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMH 412 Query: 447 EGPAGRSLIQETFDEALSFRRALANVRQNLDRNDWWFGVWQPEQVEG-------TDQVGT 499 EG +GR++ + ++ R+ + + Q++ + PE V+G T Q+ Sbjct: 413 EGVSGRNMWMDCVVNGINARKLILDNCQHI-------RPFVPELVDGKPWQSYETAQIAV 465 Query: 500 --HDWVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSA-GGKLSEQGIPAAIVSRFLW 556 + P WH F AE+ +DP K+ LTTPG+ A G+ G+PA I++ FL Sbjct: 466 DLRFFQFVPGEHWHSFEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLR 525 Query: 557 ERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGK 616 E G+V EK L S L L + K LV L+ F++ +++ PL +VLPS+ + + Sbjct: 526 ENGVVPEKCDLNSILFLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEE 585 Query: 617 RYNGVGLRDLSDAMHASYRDNATAKAMKRMYTV--LPEVAMRPSEAYDKLVRGEVEAVPI 674 RY G LR L MH Y + + K M+ P V+M P EA +RGEVE V + Sbjct: 586 RYAGYTLRQLCQEMHDLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRL 645 Query: 675 ARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFERAFPGFDSDVHGL- 733 EGRIAA +PYPPG+ ++PGE + A +L Y PGF ++ G+ Sbjct: 646 PDAEGRIAAEGALPYPPGVLCVVPGEIWGGA---VLRYFSALEEGINLLPGFAPELQGVY 702 Query: 734 --QHQDGPSGRCYTVE 747 +H CY ++ Sbjct: 703 IEEHDGRKQVWCYVIK 718 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: 1201 Number of extensions: 58 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: 732 Length adjustment: 40 Effective length of query: 711 Effective length of database: 692 Effective search space: 492012 Effective search space used: 492012 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