Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 18145 b4117 biodegradative arginine decarboxylase (RefSeq)
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__Keio:18145 Length = 755 Score = 358 bits (919), Expect = e-103 Identities = 221/678 (32%), Positives = 342/678 (50%), Gaps = 31/678 (4%) Query: 63 KAIINKADETKFNIPIFIITDDSSKVDGETMSKIFHIID---WHNNYDRRLYDREIEAAA 119 + +I K E + N+P+F++ D K + ++D W AA Sbjct: 73 RQLIGKLHERQQNVPVFLL-GDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAM 131 Query: 120 KKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDIC 179 +Y +LPP F AL Y + + PGHQGG F K+PAGR ++++YGEN+FR+D+ Sbjct: 132 TRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMG 191 Query: 180 NADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFD 239 LG LL H G ++EK+AARVF AD+++ V+ GT+ SN + A + D+V+ D Sbjct: 192 IERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVD 251 Query: 240 RNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAK 299 RN HKS+ L+ G +PVY+ SR+ YG IG IY ++ +++++KI++ K KA Sbjct: 252 RNCHKSI-EQGLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAG 310 Query: 300 RPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNL 359 + V+ TYDG YNAK+ + + D + FD AW GY +F P+ D + Sbjct: 311 QKPSYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEP 370 Query: 360 GP-DDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFY 418 G + P + T STHK SQAS IH ++ + IN +FN AYM ++TSP Y Sbjct: 371 GDHNGPTVFATHSTHKLLNALSQASYIHVREG-----RGAINFSRFNQAYMMHATTSPLY 425 Query: 419 PLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLK--------NATMIKPFLPPVV- 469 + A+ D+ M +G +G L + + +V+ R+ + + + KP+ VV Sbjct: 426 AICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVT 485 Query: 470 ---HGKPWQ--DADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDV 524 GK + DA T+ + + D W G WHGF DN +DP K + PG+ Sbjct: 486 DPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGMG- 544 Query: 525 ETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESL 584 E GE E+ G+PA ++ +L HGI+P + I+FL + T+ K LV + F+ Sbjct: 545 EDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRH 604 Query: 585 VKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQA 644 A+ PL +V+P L ++ D Y I L + + K NN E + G P Sbjct: 605 YDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYSG--LPVAE 662 Query: 645 MTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKW---TKVAQKYFL 701 +TP +A ++ NN +LV + ++ G A +PYPPGI ++ GE + Y Sbjct: 663 VTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLR 722 Query: 702 ILEESINRFPGFAPEIQG 719 L+ + FPGF E +G Sbjct: 723 SLQSWDHHFPGFEHETEG 740 Lambda K H 0.318 0.136 0.405 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: 1248 Number of extensions: 58 Number of successful extensions: 8 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: 745 Length of database: 755 Length adjustment: 40 Effective length of query: 705 Effective length of database: 715 Effective search space: 504075 Effective search space used: 504075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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