Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate HSERO_RS17280 HSERO_RS17280 lysine decarboxylase
Query= BRENDA::Q5ZH57 (745 letters) >FitnessBrowser__HerbieS:HSERO_RS17280 Length = 750 Score = 373 bits (958), Expect = e-107 Identities = 227/674 (33%), Positives = 358/674 (53%), Gaps = 26/674 (3%) Query: 63 KAIINKADETKFNIPIFII--TDDSSKVDGETMSKIFHIIDWHNNYDRRLYDREIEAAAK 120 +A +++ +IPI++ T S + + + ++ I + R I AK Sbjct: 85 RAFVSEIRHKNADIPIYLYGETRTSRHIPNDVLRELHGFIHMFEDTPE-FVARHIIREAK 143 Query: 121 KYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDICN 180 Y DG+ PPFF+AL Y + G+ + CPGH GG F KSP G+ F+ F+GE + R+D+CN Sbjct: 144 SYLDGLAPPFFRALVDYAQDGSYSWHCPGHSGGVAFLKSPVGQMFHQFFGERMLRADVCN 203 Query: 181 ADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFDR 240 A +LG LL H GP ++E++AAR+FNAD YFV NGT+TSN + + VAPGD+V+ DR Sbjct: 204 AVEELGQLLDHTGPVANSERNAARIFNADHCYFVTNGTSTSNKMVWHSTVAPGDIVVVDR 263 Query: 241 NNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKI-AKVDPEKAKAK 299 N HKS+ + +++ G PV+L +R+ G IG I ++F +SI++KI A +AK K Sbjct: 264 NCHKSILH-SIIMTGAIPVFLMPTRNHLGIIGPIPLEEFTLESIQKKIEANPFAREAKNK 322 Query: 300 RPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNL 359 +P R+ I TYDG +YN + + + + + + FD AW+ + F KD + + Sbjct: 323 KP-RILTITQSTYDGVVYNVETLKDMLDGEIETLHFDEAWLPHATFHDFYKD----MHAI 377 Query: 360 GPDDPG-----ILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSST 414 G D P I TQSTHK AG SQASQI ++S + ++ FN A++ +ST Sbjct: 378 GKDRPRAKKSLIFSTQSTHKLLAGLSQASQILVRES----ETVKLDEDAFNEAFLMHTST 433 Query: 415 SPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKPW 474 SP Y + A+ D+ A M E G L ++++ +++ R+ + K V G Sbjct: 434 SPQYSIIASCDVAAAMMEAPGGTALVEESILEALDFRRAMKKIDQEFGDEWWFQVWGPNS 493 Query: 475 QDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFGI 534 AD + + + W + WHGF A +DP K + PG+ + G++ + GI Sbjct: 494 FAADG---IGEREDWVIKAEDDWHGFGNLAPGFNMLDPIKATIVNPGLAL-NGQFGETGI 549 Query: 535 PAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDEV 594 PA I+ YL EHG+I EK L S + T T+ + + LVT + +F+ + P+ + Sbjct: 550 PASIVTKYLAEHGVIVEKCGLYSFFIMFTIGITKGRWNTLVTALQQFKDDYDKNQPIWRI 609 Query: 595 LPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVEL 654 LP +++ RYE ++ LCQ++H+ Y+ + EM+L P AM P A ++ Sbjct: 610 LPE-FAQRNPRYERLGLRDLCQQIHETYRAYDVARLTTEMYLSDMQP--AMKPSDAFSKM 666 Query: 655 LKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQKYFLILEESINRFPGFA 714 + VPL ++EG PYPPGI ++PGE + K Y + +FPGF Sbjct: 667 AHREIERVPLDELEGRVTSILLTPYPPGIPLLIPGEIFNKTIVDYLKFARDFNEKFPGFE 726 Query: 715 PEIQGVYFEKENGK 728 ++ G+ + NG+ Sbjct: 727 TDVHGLVKREVNGR 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: 1257 Number of extensions: 62 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: 750 Length adjustment: 40 Effective length of query: 705 Effective length of database: 710 Effective search space: 500550 Effective search space used: 500550 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